大家如果在github上面下載ACPYPE （https://github.com/t-/acpype），放入到LINUX上面安裝後，百分百報錯，出現的問題如下：
[root@pdynamo test]# ../acpype.py -i FFF.pdb
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2020 AWSdS |
============================================================================
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
==> * Antechamber OK *
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `which: no parmchk in (/usr/local/bin:/home/peter/Amber/amber18/bin:/home/peter/gmx2019.4/bin:/home/peter/fftw-3.3.8/bin:/home/peter/openmpi-3.1.3/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/home/peter/intel/debugger_2019/gdb/intel64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/home/peter/Amber/amber18/bin:/root/bin) -i FFF_bcc_gaff.mol2 -f mol2 -o FFF_AC.frcmod'
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `which: no sleap in (/usr/local/bin:/home/peter/Amber/amber18/bin:/home/peter/gmx2019.4/bin:/home/peter/fftw-3.3.8/bin:/home/peter/openmpi-3.1.3/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/bin:/home/peter/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/home/peter/intel/debugger_2019/gdb/intel64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/home/peter/Amber/amber18/bin:/root/bin) -f sleap.in'
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'FFF_AC.prmtop'
Total time of execution: 3m 8s
其原因是這個源文件有毛病，請大家把底下這個複製，然後覆蓋acpepy.py這個文件，直接就好用。
這個文件感謝計算化學領域國內最強的盧天大神提供：http://bbs.keinsci.com/thread-14021-1-1.html
#!/usr/bin/env python
from __future__ import print_function
from datetime import datetime
from shutil import copy2
from shutil import rmtree
import traceback
import signal
import time
import optparse
import math
import os
import pickle
import sys
import subprocess as sub
import re
"""
Requirements: Python 2.6 or higher or Python 3.x
Antechamber (from AmberTools preferably)
OpenBabel (optional, but strongly recommended)
This code is released under GNU General Public License V3.
<<< NO WARRANTY AT ALL!!! >>>
It was inspired by:
- amb2gmx.pl (Eric Sorin, David Mobley and John Chodera)
and depends on Antechamber and Openbabel
- YASARA Autosmiles:
http://www.yasara.org/autosmiles.htm (Elmar Krieger)
- topolbuild (Bruce Ray)
- xplo2d (G.J. Kleywegt)
For Antechamber, please cite:
1. Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and
bond type perception in molecular mechanical calculations". Journal of
Molecular Graphics and Modelling , 25, 2006, 247260.
2. Wang, J., Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A.
"Development and testing of a general AMBER force field". Journal of
Computational Chemistry, 25, 2004, 1157-1174.
If you use this code, I am glad if you cite:
SOUSA DA SILVA, A. W. & VRANKEN, W. F.
ACPYPE - AnteChamber PYthon Parser interfacE.
BMC Research Notes 2012, 5:367 doi:10.1186/1756-0500-5-367
http://www.biomedcentral.com/1756-0500/5/367
Alan Wilter Sousa da Silva, D.Sc.
Bioinformatician, UniProt, EMBL-EBI
Hinxton, Cambridge CB10 1SD, UK.
>>http://www.ebi.ac.uk/~awilter<<
alanwilter _at_ gmail _dot_ com
"""
svnId = '$Id$'
try:
svnRev, svnDate, svnTime = svnId.split()[2:5]
except:
svnRev, svnDate, svnTime = '0', '0', '0'
year = datetime.today().year
tag = "%s %s Rev: %s" % (svnDate, svnTime, svnRev)
lineHeader = \
'''
| ACPYPE: AnteChamber PYthon Parser interfacE v. %s (c) %s AWSdS |
''' % (tag, year)
frameLine = (len(lineHeader) - 2) * '='
header = '%s%s%s' % (frameLine, lineHeader, frameLine)
# TODO:
# Howto Charmm and Amber with NAMD
# Howto build topology for a modified amino acid
# CYANA topology files
# List of Topology Formats created by acpype so far:
outTopols = ['gmx', 'cns', 'charmm']
qDict = {'mopac': 0, 'divcon': 1, 'sqm': 2}
# Residues that are not solute, to be avoided when balancing charges in
# amb2gmx mode
ionOrSolResNameList = ['Cl-', 'Na+', 'K+', 'CIO', 'Cs+', 'IB', 'Li+', 'MG2',
'Rb+', 'WAT', 'MOH', 'NMA']
# leapAmberFile = 'leaprc.ff99SB' # 'leaprc.ff10' and 'leaprc.ff99bsc0' has extra Atom Types not in parm99.dat
leapAmberFile = 'leaprc.protein.ff14SB' # 'leaprc.ff14SB'
# "qm_theory='AM1', grms_tol=0.0002, maxcyc=999, tight_p_conv=1, scfconv=1.d-10,"
# "AM1 ANALYT MMOK GEO-OK PRECISE"
cal = 4.184
Pi = 3.141593
qConv = 18.222281775 # 18.2223
radPi = 57.295780 # 180/Pi
maxDist = 3.0
minDist = 0.5
maxDist2 = maxDist ** 2 # squared Ang.
minDist2 = minDist ** 2 # squared Ang.
diffTol = 0.01
dictAmbAtomType2AmbGmxCode = \
{'BR': '1', 'C': '2', 'CA': '3', 'CB': '4', 'CC': '5', 'CK': '6', 'CM': '7', 'CN': '8', 'CQ': '9',
'CR': '10', 'CT': '11', 'CV': '12', 'CW': '13', 'C*': '14', 'Ca': '15', 'F': '16', 'H': '17',
'HC': '18', 'H1': '19', 'H2': '20', 'H3': '21', 'HA': '22', 'H4': '23', 'H5': '24', 'HO': '25',
'HS': '26', 'HW': '27', 'HP': '28', 'I': '29', 'Cl': '30', 'Na': '31', 'IB': '32', 'Mg': '33',
'N': '34', 'NA': '35', 'NB': '36', 'NC': '37', 'N2': '38', 'N3': '39', 'N*': '40', 'O': '41',
'OW': '42', 'OH': '43', 'OS': '44', 'O2': '45', 'P': '46', 'S': '47', 'SH': '48', 'CU': '49',
'FE': '50', 'K': '51', 'Rb': '52', 'Cs': '53', 'Li': '56', 'Zn': '57', 'Sr': '58', 'Ba': '59',
'MCH3A': 'MCH3A', 'MCH3B': 'MCH3B', 'MNH2': 'MNH2', 'MNH3': 'MNH3', 'MW': 'MW'}
dictOplsAtomType2OplsGmxCode = \
{'Ac3+': ['697'], 'Am3+': ['699'], 'Ar': ['Ar', '097'], 'Ba2+': ['414'],
'Br': ['722', '730'], 'Br-': ['402'],
'CT': ['064', '076', '122', '135', '136', '137', '138', '139', '148', '149', '152', '157', '158', '159', '161', '173', '174', '175', '181', '182', '183', '184', '206', '207', '208', '209', '210', '211', '212', '213', '214', '215', '216', '217', '218', '219', '220', '223', '224', '225', '229', '230', '242', '243', '244', '256', '257', '258', '259', '273', '274', '275', '276', '291', '292', '293', '294', '297', '305', '306', '307', '308', '331', '371', '373', '375', '391', '396', '421', '431', '443', '448', '453', '455', '458', '461', '468', '476', '482', '484', '486', '490', '491', '492', '498', '499', '505', '515', '516', '645', '670', '671', '672', '673', '674', '675', '676', '677', '678', '679', '680', '681', '701', '725', '747', '748', '755', '756', '757', '758', '762', '764', '765', '766', '774', '775', '776', '782', '783', '903', '904', '905', '906', '907', '908', '912', '913', '914', '915', '942', '943', '944', '945', '951', '957', '959', '960', '961', '962', '963', '964'],
'CA': ['053', '145', '147', '166', '199', '221', '228', '260', '263', '266', '302', '312', '315', '317', '336', '351', '362', '380', '457', '460', '463', '472', '488', '521', '522', '523', '528', '532', '533', '538', '539', '551', '582', '590', '591', '592', '593', '604', '605', '606', '607', '608', '609', '610', '611', '612', '625', '644', '647', '648', '649', '650', '651', '652', '714', '716', '718', '720', '724', '727', '729', '731', '735', '736', '737', '738', '739', '742', '752', '768', '916', '917', '918'],
'C3': ['007', '010', '036', '039', '063', '065', '067', '068', '069', '070', '080', '088', '090', '092', '096', '106', '107', '109', '126', '132', '415', '418', '425', '429'],
'C': ['001', '017', '026', '058', '095', '131', '231', '234', '235', '247', '252', '267', '320', '322', '334', '366', '378', '470', '471', '772', '952'],
'C2': ['005', '009', '015', '016', '019', '022', '027', '028', '031', '034', '037', '056', '057', '061', '071', '081', '089', '091', '093', '110'],
'CT_2': ['223B', '224B', '225B', '246', '283', '284', '285', '292B', '293B', '295', '298', '299', '906B', '912B'],
'CM': ['141', '142', '143', '227', '323', '324', '337', '338', '381', '382', '517', '518', '708'],
'CW': ['508', '514', '543', '552', '561', '567', '575', '583', '588', '637'],
'CB': ['050', '349', '350', '364', '365', '501', '595', '623', '624'],
'CH': ['006', '008', '014', '025', '029', '030', '060', '073'],
'CZ': ['261', '423', '754', '925', '927', '928', '929', '931'],
'CO': ['189', '191', '193', '195', '197', '198'],
'C_2': ['232', '233', '277', '280', '465'],
'CR': ['506', '509', '558', '572', '634'],
'CQ': ['347', '531', '621', '642'],
'CV': ['507', '560', '574', '636'],
'CY': ['711', '712', '713', '733'],
'CS': ['544', '568', '589'],
'CK': ['353', '627'], 'CN': ['502', '594'], 'CP': ['043', '048'], 'CU': ['550', '581'],
'CT_3': ['245', '296'], 'C=': ['150', '178'], 'CD': ['011', '075'],
'C4': ['066'], 'C7': ['077'], 'C8': ['074'], 'C9': ['072'], 'CX': ['510'],
'C!': ['145B'], 'C*': ['500'], 'C+': ['700'], 'C_3': ['271'],
'CC': ['045'], 'CF': ['044'], 'CG': ['049'], 'CT_4': ['160'],
'Ca2+': ['412'],
'Cl': ['123', '151', '226', '264'],
'Cl-': ['401', '709'],
'Cs+': ['410'], 'Cu2+': ['Cu2+'], 'Eu3+': ['705'],
'F': ['164', '719', '721', '726', '728', '786', '956', '965'],
'F-': ['400'], 'Fe2+': ['Fe2+'], 'Gd3+': ['706'],
'HA': ['146', '316', '318', '389', '524', '525', '526', '529', '534', '535', '536', '540', '541', '546', '547', '554', '555', '556', '563', '564', '565', '569', '570', '576', '577', '578', '584', '585', '586', '597', '598', '599', '600', '601', '602', '613', '614', '615', '616', '617', '618', '619', '629', '630', '631', '638', '639', '640', '643', '653', '654', '655', '656', '715', '717', '740', '741', '746'],
'HC': ['140', '144', '153', '156', '165', '176', '185', '190', '192', '194', '196', '255', '279', '282', '329', '330', '332', '344', '372', '374', '376', '392', '416', '419', '422', '426', '430', '432', '444', '449', '454', '456', '459', '462', '469', '477', '483', '485', '487', '702', '710', '759', '763', '777', '778', '779', '784', '911', '926', '930', '950', '958'],
'H': ['004', '013', '041', '047', '128', '240', '241', '250', '254', '314', '325', '327', '339', '342', '343', '357', '358', '360', '367', '369', '383', '385', '387', '388', '428', '479', '481', '504', '513', '545', '553', '562', '596', '632', '744', '745', '909', '910'],
'H3': ['021', '052', '055', '104', '105', '289', '290', '301', '304', '310', '941', '955'],
'HO': ['024', '079', '155', '163', '168', '170', '172', '188', '270', '435'],
'HS': ['033', '086', '087', '204', '205'],
'HW': ['112', '114', '117', '119', '796'],
'H4': ['345', '390'], 'H5': ['355', '359'],
'He': ['130'], 'I': ['732'], 'I-': ['403'], 'K+': ['408'], 'Kr': ['098'],
'LP': ['433', '797'], 'La3+': ['703'], 'Li+': ['404', '406'],
'MCH3A': ['MCH3A'], 'MCH3B': ['MCH3B'], 'MNH2': ['MNH2'], 'MNH3': ['MNH3'],
'MW': ['MW', '115'], 'Mg2+': ['411'],
'NA': ['040', '046', '319', '321', '333', '354', '361', '377', '379', '503', '512', '542', '548', '557', '587', '628'],
'NC': ['311', '335', '346', '348', '363', '520', '527', '530', '537', '603', '620', '622', '641', '646'],
'N': ['003', '012', '094', '237', '238', '239', '249', '251', '265', '478', '480', '787'],
'N3': ['020', '101', '102', '103', '286', '287', '288', '309', '427', '940', '953'],
'N2': ['051', '054', '300', '303', '313', '341', '356', '368', '386', '743'],
'NB': ['042', '352', '511', '549', '559', '573', '580', '626', '635'],
'N*': ['319B', '333B', '354B', '377B'],
'NT': ['127', '900', '901', '902'],
'NZ': ['262', '424', '750', '753'],
'NO': ['760', '767'], 'NY': ['749', '751'],
'Na+': ['405', '407'], 'Nd3+': ['704'], 'Ne': ['129'],
'OS': ['062', '108', '179', '180', '186', '395', '442', '447', '452', '467', '473', '566', '571', '579', '773'],
'O': ['002', '059', '236', '248', '253', '326', '328', '340', '370', '384', '771', '788'],
'OH': ['023', '078', '154', '162', '167', '169', '171', '187', '268', '420', '434'],
'O2': ['018', '125', '272', '394', '441', '446', '451', '954'],
'OW': ['111', '113', '116', '118', '795'],
'O_2': ['278', '281', '466'],
'OY': ['475', '494', '497'],
'OL': ['120'], 'ON': ['761'], 'OU': ['437'], 'O_3': ['269'],
'P': ['393', '440', '445', '450', '785'],
'P+': ['781'], 'Rb+': ['409'],
'S': ['035', '038', '084', '085', '124', '202', '203', '222', '633'],
'SH': ['032', '082', '083', '200', '201', '417', '734'],
'SI': ['SI'], 'SY': ['474'], 'SY2': ['493'], 'SZ': ['496'], 'Sr2+': ['413'],
'Th4+': ['698'], 'U': ['436'], 'Xe': ['099'], 'Yb3+': ['707'], 'Zn2+': ['Zn2+']}
# reverse dictOplsAtomType2OplsGmxCode
oplsCode2AtomTypeDict = {}
for k, v in list(dictOplsAtomType2OplsGmxCode.items()):
for code in v:
oplsCode2AtomTypeDict[code] = k
# if code in oplsCode2AtomTypeDict.keys():
# oplsCode2AtomTypeDict[code].append(k)
# else:
# oplsCode2AtomTypeDict[code] = [k]
# Cross dictAmbAtomType2AmbGmxCode with dictOplsAtomType2OplsGmxCode & add H1,HP,H2
dictAtomTypeAmb2OplsGmxCode = {'H1': ['140', '1.00800'], 'HP': ['140', '1.00800'], 'H2': ['140', '1.00800']}
dictOplsMass = {'SY2': ['32.06000'], 'Zn2+': ['65.37000'], 'CQ': ['12.01100'], 'CP': ['12.01100'], 'Nd3+': ['144.24000'], 'Br-': ['79.90400'], 'Cu2+': ['63.54600'], 'Br': ['79.90400'], 'H': ['1.00800'], 'P': ['30.97376'], 'Sr2+': ['87.62000'], 'ON': ['15.99940'], 'OL': ['0.00000'], 'OH': ['15.99940'], 'OY': ['15.99940'], 'OW': ['15.99940'], 'OU': ['15.99940'], 'OS': ['15.99940'], 'Am3+': ['243.06000'], 'HS': ['1.00800'], 'HW': ['1.00800'], 'HO': ['1.00800'], 'HC': ['1.00800'], 'HA': ['1.00800'], 'O2': ['15.99940'], 'Ca2+': ['40.08000'], 'Th4+': ['232.04000'], 'He': ['4.00260'], 'C': ['12.01100'], 'Cs+': ['132.90540'], 'O': ['15.99940'], 'Gd3+': ['157.25000'], 'S': ['32.06000'], 'P+': ['30.97376'], 'La3+': ['138.91000'], 'H3': ['1.00800'], 'H4': ['1.00800'], 'MNH2': ['0.00000'], 'MW': ['0.00000'], 'NB': ['14.00670'], 'K+': ['39.09830'], 'Ne': ['20.17970'], 'Rb+': ['85.46780'], 'C+': ['12.01100'], 'C*': ['12.01100'], 'NO': ['14.00670'], 'CT_4': ['12.01100'], 'NA': ['14.00670'], 'C!': ['12.01100'], 'NC': ['14.00670'], 'NZ': ['14.00670'], 'CT_2': ['12.01100'], 'CT_3': ['12.01100'], 'NY': ['14.00670'], 'C9': ['14.02700'], 'C8': ['13.01900'], 'C=': ['12.01100'], 'Yb3+': ['173.04000'], 'C3': ['15.03500', '12.01100'], 'C2': ['14.02700'], 'C7': ['12.01100'], 'C4': ['16.04300'], 'CK': ['12.01100'], 'Cl-': ['35.45300'], 'N*': ['14.00670'], 'CH': ['13.01900'], 'CO': ['12.01100'], 'CN': ['12.01100'], 'CM': ['12.01100'], 'F': ['18.99840'], 'CC': ['12.01100'], 'CB': ['12.01100'], 'CA': ['12.01100'], 'CG': ['12.01100'], 'CF': ['12.01100'], 'N': ['14.00670'], 'CZ': ['12.01100'], 'CY': ['12.01100'], 'CX': ['12.01100'], 'Ac3+': ['227.03000'], 'CS': ['12.01100'], 'CR': ['12.01100'], 'N2': ['14.00670'], 'N3': ['14.00670'], 'CW': ['12.01100'], 'CV': ['12.01100'], 'CU': ['12.01100'], 'CT': ['12.01100'], 'SZ': ['32.06000'], 'SY': ['32.06000'], 'Cl': ['35.45300'], 'NT': ['14.00670'], 'O_2': ['15.99940'], 'Xe': ['131.29300'], 'SI': ['28.08000'], 'SH': ['32.06000'], 'Eu3+': ['151.96000'], 'F-': ['18.99840'], 'MNH3': ['0.00000'], 'H5': ['1.00800'], 'C_3': ['12.01100'], 'C_2': ['12.01100'], 'I-': ['126.90450'], 'LP': ['0.00000'], 'I': ['126.90450'], 'Na+': ['22.98977'], 'Li+': ['6.94100'], 'U': ['0.00000'], 'MCH3A': ['0.00000'], 'MCH3B': ['0.00000'], 'CD': ['13.01900', '12.01100'], 'O_3': ['15.99940'], 'Kr': ['83.79800'], 'Fe2+': ['55.84700'], 'Ar': ['39.94800'], 'Mg2+': ['24.30500'], 'Ba2+': ['137.33000']}
for ambKey in dictAmbAtomType2AmbGmxCode:
if ambKey in dictOplsAtomType2OplsGmxCode:
dictAtomTypeAmb2OplsGmxCode[ambKey] = dictOplsAtomType2OplsGmxCode[ambKey] + list(dictOplsMass[ambKey])
# learnt from 22 residues test.
dictAtomTypeAmb2OplsGmxCode = {'HS': ['204', '1.008'], 'HP': ['140', '1.008'], 'HO': ['155', '168', '1.008'], 'HC': ['140', '1.008'], 'HA': ['146', '1.008'], 'O2': ['272', '15.9994'], 'C*': ['500', '12.011'], 'NA': ['503', '512', '14.0067'], 'NB': ['511', '14.0067'], 'CB': ['501', '12.011'], 'C': ['235', '271', '12.011'], 'CN': ['502', '12.011'], 'CM': ['302', '12.011'], 'CC': ['507', '508', '510', '12.011'], 'H': ['240', '241', '290', '301', '304', '310', '504', '513', '1.008'], 'CA': ['145', '166', '12.011'], 'O': ['236', '15.9994'], 'N': ['237', '238', '239', '14.0067'], 'S': ['202', '32.06'], 'CR': ['506', '509', '12.011'], 'N2': ['300', '303', '14.0067'], 'N3': ['287', '309', '14.0067'], 'CW': ['508', '510', '514', '12.011'], 'CV': ['507', '12.011'], 'CT': ['135', '136', '137', '149', '157', '158', '206', '209', '210', '223B', '224B', '245', '246', '274', '283', '284', '285', '292', '292B', '293B', '296', '307', '308', '505', '12.011'], 'OH': ['154', '167', '15.9994'], 'H1': ['140', '1.008'], 'H4': ['146', '1.008'], 'H5': ['146', '1.008'], 'SH': ['200', '32.06']}
# learnt from 22 residues test.
dictAtomTypeGaff2OplsGmxCode = {'cc': ['500', '506', '507', '508', '514', '12.011'], 'ca': ['145', '166', '501', '502', '12.011'], 'h1': ['140', '1.008'], 'h4': ['146', '1.008'], 'h5': ['146', '1.008'], 'cz': ['302', '12.011'], 'c2': ['509', '510', '12.011'], 'nh': ['300', '303', '14.0067'], 'ha': ['146', '1.008'], 'na': ['503', '512', '14.0067'], 'nc': ['511', '14.0067'], 'nd': ['511', '14.0067'], 'hx': ['140', '1.008'], 'hs': ['204', '1.008'], 'hn': ['240', '241', '290', '301', '304', '310', '504', '513', '1.008'], 'ho': ['155', '168', '1.008'], 'c3': ['135', '136', '137', '149', '157', '158', '206', '209', '210', '223B', '224B', '245', '246', '274', '283', '284', '285', '292', '292B', '293B', '296', '307', '308', '505', '12.011'], 'hc': ['140', '1.008'], 'cd': ['500', '506', '507', '508', '514', '12.011'], 'c': ['235', '271', '12.011'], 'oh': ['154', '167', '15.9994'], 'ss': ['202', '32.06'], 'o': ['236', '272', '15.9994'], 'n': ['237', '238', '239', '14.0067'], 'sh': ['200', '32.06'], 'n4': ['287', '309', '14.0067']}
# draft
atomTypeAmber2oplsDict = {'HS': ['HS'], 'HP': ['HC'], 'HO': ['HO'], 'HC': ['HC'],
'HA': ['HA'], 'O2': ['O2'], 'C*': ['C*'], 'NA': ['NA'],
'NB': ['NB'], 'CB': ['CB'], 'CN': ['CN'], 'CV': ['CV'],
'CM': ['CA'], 'CA': ['CA'], 'CR': ['CR'], 'OH': ['OH'],
'H1': ['HC'], 'H4': ['HA'], 'N2': ['N2'], 'N3': ['N3'],
'H5': ['HA'], 'SH': ['SH'], 'N': ['N'], 'S': ['S'], 'O': ['O'],
'C': ['C', 'C_3'], 'CW': ['CW', 'CX'], 'H': ['H', 'H3'],
'CC': ['CX', 'CW', 'CV'], 'CT': ['CT', 'CT_2', 'CT_3']}
# draft
a2oD = {'amber99_2': ['opls_235', 'opls_271'],
'amber99_3': ['opls_302', 'opls_145'],
'amber99_5': ['opls_507', 'opls_508', 'opls_510'],
'amber99_11': ['opls_209', 'opls_158', 'opls_283', 'opls_223B', 'opls_293B',
'opls_284', 'opls_292B', 'opls_274', 'opls_136', 'opls_135',
'opls_292', 'opls_157', 'opls_206', 'opls_137', 'opls_505',
'opls_224B', 'opls_307', 'opls_308', 'opls_210', 'opls_149'],
'amber99_13': ['opls_514'],
'amber99_14': ['opls_500'],
'amber99_17': ['opls_504', 'opls_241', 'opls_240', 'opls_290', 'opls_301',
'opls_310', 'opls_304', 'opls_513'],
'amber99_18': ['opls_140'],
'amber99_19': ['opls_140'],
'amber99_22': ['opls_146'],
'amber99_23': ['opls_146'],
'amber99_25': ['opls_155'],
'amber99_26': ['opls_204'],
'amber99_28': ['opls_140'],
'amber99_34': ['opls_238', 'opls_239', 'opls_237'],
'amber99_35': ['opls_512', 'opls_503'],
'amber99_36': ['opls_511'],
'amber99_38': ['opls_300', 'opls_303'],
'amber99_39': ['opls_309', 'opls_287'],
'amber99_41': ['opls_236'],
'amber99_43': ['opls_154'],
'amber99_45': ['opls_272'],
'amber99_47': ['opls_202'],
'amber99_48': ['opls_200'],
}
global pid
pid = 0
head = "%s created by acpype (Rev: " + svnRev + ") on %s\n"
date = datetime.now().ctime()
usage = \
"""
acpype -i _file_ [-c _string_] [-n _int_] [-m _int_] [-a _string_] [-f] etc. or
acpype -p _prmtop_ -x _inpcrd_ [-d]"""
epilog = \
"""
output: assuming 'root' is the basename of either the top input file,
the 3-letter residue name or user defined (-b option)
root_bcc_gaff.mol2: final mol2 file with 'bcc' charges and 'gaff' atom type
root_AC.inpcrd : coord file for AMBER
root_AC.prmtop : topology and parameter file for AMBER
root_AC.lib : residue library file for AMBER
root_AC.frcmod : modified force field parameters
root_GMX.gro : coord file for GROMACS
root_GMX.top : topology file for GROMACS
root_GMX.itp : molecule unit topology and parameter file for GROMACS
root_GMX_OPLS.itp : OPLS/AA mol unit topol & par file for GROMACS (experimental!)
em.mdp, md.mdp : run parameters file for GROMACS
root_NEW.pdb : final pdb file generated by ACPYPE
root_CNS.top : topology file for CNS/XPLOR
root_CNS.par : parameter file for CNS/XPLOR
root_CNS.inp : run parameters file for CNS/XPLOR
root_CHARMM.rtf : topology file for CHARMM
root_CHARMM.prm : parameter file for CHARMM
root_CHARMM.inp : run parameters file for CHARMM"""
SLEAP_TEMPLATE = \
"""
source %(leapAmberFile)s
source %(leapGaffFile)s
set default fastbld on
#set default disulfide auto
%(res)s = loadpdb %(baseOrg)s.pdb
#check %(res)s
saveamberparm %(res)s %(acBase)s.prmtop %(acBase)s.inpcrd
saveoff %(res)s %(acBase)s.lib
quit
"""
TLEAP_TEMPLATE = \
"""
verbosity 1
source %(leapAmberFile)s
source %(leapGaffFile)s
mods = loadamberparams %(acBase)s.frcmod
%(res)s = loadmol2 %(acMol2FileName)s
check %(res)s
saveamberparm %(res)s %(acBase)s.prmtop %(acBase)s.inpcrd
saveoff %(res)s %(acBase)s.lib
quit
"""
def dotproduct(aa, bb):
return sum((a * b) for a, b in zip(aa, bb))
def crosproduct(a, b):
c = [a[1] * b[2] - a[2] * b[1],
a[2] * b[0] - a[0] * b[2],
a[0] * b[1] - a[1] * b[0]]
return c
def length(v):
return math.sqrt(dotproduct(v, v))
def vec_sub(aa, bb):
return [a - b for a, b in zip(aa, bb)]
def imprDihAngle(a, b, c, d):
ba = vec_sub(a, b)
bc = vec_sub(c, b)
cb = vec_sub(b, c)
cd = vec_sub(d, c)
n1 = crosproduct(ba, bc)
n2 = crosproduct(cb, cd)
angle = math.acos(dotproduct(n1, n2) / (length(n1) * length(n2))) * 180 / Pi
cp = crosproduct(n1, n2)
if (dotproduct(cp, bc) < 0):
angle = -1 * angle
return angle
def invalidArgs(text=None):
if text:
print('ERROR: ' + text)
sys.exit(1)
# verNum = string.split(sys.version)[0]
verNum = re.sub('[^0-9\.]', '', sys.version.split()[0])
version = verNum.split('.') # string.split(verNum, ".")
verList = list(map(int, version))
if verList < [2, 6, 0]:
invalidArgs(text="Python version %s\n Sorry, you need python 2.6 or higher" % verNum)
try:
set()
except NameError:
from sets import Set as set # @UnresolvedImport
def elapsedTime(seconds, suffixes=['y', 'w', 'd', 'h', 'm', 's'], add_s=False, separator=' '):
"""
Takes an amount of seconds and turns it into a human-readable amount of time.
"""
# the formatted time string to be returned
time = []
# the pieces of time to iterate over (days, hours, minutes, etc)
# - the first piece in each tuple is the suffix (d, h, w)
# - the second piece is the length in seconds (a day is 60s * 60m * 24h)
parts = [(suffixes[0], 60 * 60 * 24 * 7 * 52),
(suffixes[1], 60 * 60 * 24 * 7),
(suffixes[2], 60 * 60 * 24),
(suffixes[3], 60 * 60),
(suffixes[4], 60),
(suffixes[5], 1)]
# for each time piece, grab the value and remaining seconds, and add it to
# the time string
for suffix, length in parts:
value = seconds // length
if value > 0:
seconds = seconds % length
time.append('%s%s' % (str(value),
(suffix, (suffix, suffix + 's')[value > 1])[add_s]))
if seconds < 1:
break
return separator.join(time)
def splitBlock(dat):
'''split a amber parm dat file in blocks
0 = mass, 1 = extra + bond, 2 = angle, 3 = dihedral, 4 = improp, 5 = hbond
6 = equiv nbon, 7 = nbon, 8 = END, 9 = etc.
'''
dict_ = {}
count = 0
for line in dat:
line = line.rstrip()
if count in dict_:
dict_[count].append(line)
else:
dict_[count] = [line]
if not line:
count += 1
return dict_
def getParCode(line):
key = line.replace(' -', '-').replace('- ', '-').split()[0]
return key
def parseFrcmod(lista):
heads = ['MASS', 'BOND', 'ANGL', 'DIHE', 'IMPR', 'HBON', 'NONB']
dict_ = {}
for line in lista[1:]:
line = line.strip()
if line[:4] in heads:
head = line[:4]
dict_[head] = []
dd = {}
continue
elif line:
key = line.replace(' -', '-').replace('- ', '-').split()[0]
if key in dd:
if not dd[key].count(line):
dd[key].append(line)
else:
dd[key] = [line]
dict_[head] = dd
for k in dict_.keys():
if not dict_[k]:
dict_.pop(k)
return dict_
def parmMerge(fdat1, fdat2, frcmod=False):
'''merge two amber parm dat/frcmod files and save in /tmp'''
name1 = os.path.basename(fdat1).split('.dat')[0]
if frcmod:
name2 = os.path.basename(fdat2).split('.')[1]
else:
name2 = os.path.basename(fdat2).split('.dat')[0]
mname = '/tmp/' + name1 + name2 + '.dat'
mdatFile = open(mname, 'w')
mdat = ['merged %s %s' % (name1, name2)]
# if os.path.exists(mname): return mname
dat1 = splitBlock(open(fdat1).readlines())
if frcmod:
dHeads = {'MASS': 0, 'BOND': 1, 'ANGL': 2, 'DIHE': 3, 'IMPR': 4, 'HBON': 5, 'NONB': 7}
dat2 = parseFrcmod(open(fdat2).readlines()) # dict
for k in dat2:
for parEntry in dat2[k]:
idFirst = None
for line in dat1[dHeads[k]][:]:
if line:
key = line.replace(' -', '-').replace('- ', '-').split()[0]
if key == parEntry:
if not idFirst:
idFirst = dat1[dHeads[k]].index(line)
dat1[dHeads[k]].remove(line)
rev = dat2[k][parEntry][:]
rev.reverse()
if idFirst is None:
idFirst = 0
for ll in rev:
if dHeads[k] in [0, 1, 7]: # MASS has title in index 0 and so BOND, NONB
dat1[dHeads[k]].insert(idFirst + 1, ll)
else:
dat1[dHeads[k]].insert(idFirst, ll)
dat1[0][0] = mdat[0]
for k in dat1:
for line in dat1[k]:
mdatFile.write(line + '\n')
return mname
dat2 = splitBlock(open(fdat2).readlines())
for k in dat1.keys()[:8]:
if k == 0:
lines = dat1[k][1:-1] + dat2[k][1:-1] + ['']
for line in lines:
mdat.append(line)
if k == 1:
for i in dat1[k]:
if '-' in i:
id1 = dat1[k].index(i)
break
for j in dat2[k]:
if '-' in j:
id2 = dat2[k].index(j)
break
l1 = dat1[k][:id1]
l2 = dat2[k][:id2]
line = ''
for item in l1 + l2:
line += item.strip() + ' '
mdat.append(line)
lines = dat1[k][id1:-1] + dat2[k][id2:-1] + ['']
for line in lines:
mdat.append(line)
if k in [2, 3, 4, 5, 6]: # angles, p dih, imp dih
lines = dat1[k][:-1] + dat2[k][:-1] + ['']
for line in lines:
mdat.append(line)
if k == 7:
lines = dat1[k][:-1] + dat2[k][1:-1] + ['']
for line in lines:
mdat.append(line)
for k in dat1.keys()[8:]:
for line in dat1[k]:
mdat.append(line)
for k in dat2.keys()[9:]:
for line in dat2[k]:
mdat.append(line)
for line in mdat:
mdatFile.write(line + '\n')
mdatFile.close()
return mname
def _getoutput(cmd):
'''to simulate commands.getoutput in order to work with python 2.6 up to 3.x'''
out = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE).communicate()[0][:-1]
try:
o = str(out.decode())
except:
o = str(out)
return o
class AbstractTopol(object):
"""
Super class to build topologies
"""
def __init__(self):
if self.__class__ is AbstractTopol:
raise TypeError("Attempt to create istance of abstract class AbstractTopol")
def printDebug(self, text=''):
if self.debug:
print('DEBUG: %s' % text)
def printWarn(self, text=''):
if self.verbose:
print('WARNING: %s' % text)
def printError(self, text=''):
if self.verbose:
print('ERROR: %s' % text)
def printMess(self, text=''):
if self.verbose:
print('==> %s' % text)
def printQuoted(self, text=''):
if self.verbose:
print(10 * '+' + 'start_quote' + 59 * '+')
print(text)
print(10 * '+' + 'end_quote' + 61 * '+')
def guessCharge(self):
"""
Guess the charge of a system based on antechamber
Returns None in case of error
"""
done = False
error = False
charge = self.chargeVal
localDir = os.path.abspath('.')
if not os.path.exists(self.tmpDir):
os.mkdir(self.tmpDir)
if not os.path.exists(os.path.join(self.tmpDir, self.inputFile)):
copy2(self.absInputFile, self.tmpDir)
os.chdir(self.tmpDir)
if self.chargeType == 'user':
if self.ext == '.mol2':
self.printMess("Reading user's charges from mol2 file...")
charge = self.readMol2TotalCharge(self.inputFile)
done = True
else:
self.printWarn("cannot read charges from a PDB file")
self.printWarn("using now 'bcc' method for charge")
if self.chargeVal is None and not done:
self.printWarn("no charge value given, trying to guess one...")
mol2FileForGuessCharge = self.inputFile
if self.ext == ".pdb":
cmd = '%s -ipdb %s -omol2 %s.mol2' % (self.babelExe, self.inputFile,
self.baseName)
self.printDebug("guessCharge: " + cmd)
out = _getoutput(cmd)
self.printDebug(out)
mol2FileForGuessCharge = os.path.abspath(self.baseName + ".mol2")
in_mol = 'mol2'
else:
in_mol = self.ext[1:]
if in_mol == 'mol':
in_mol = 'mdl'
cmd = '%s -i %s -fi %s -o tmp -fo mol2 -c gas -pf y' % \
(self.acExe, mol2FileForGuessCharge, in_mol)
if self.debug:
self.printMess("Debugging...")
cmd = cmd.replace('-pf y', '-pf n')
print(cmd)
log = _getoutput(cmd).strip()
if os.path.exists('tmp'):
charge = self.readMol2TotalCharge('tmp')
else:
try:
charge = float(log.strip().split('equal to the total charge (')[-1].split(') based on Gasteiger atom type, exit')[0])
except:
error = True
if error:
self.printError("guessCharge failed")
os.chdir(localDir)
self.printQuoted(log)
self.printMess("Trying with net charge = 0 ...")
# self.chargeVal = 0
return None
charge = float(charge)
charge2 = int(round(charge))
drift = abs(charge2 - charge)
self.printDebug("Net charge drift '%3.6f'" % drift)
if drift > diffTol:
self.printError("Net charge drift '%3.5f' bigger than tolerance '%3.5f'" % (drift, diffTol))
if not self.force:
sys.exit(1)
self.chargeVal = str(charge2)
self.printMess("... charge set to %i" % charge2)
os.chdir(localDir)
def setResNameCheckCoords(self):
"""Set a 3 letter residue name
and check coords duplication
"""
exit_ = False
localDir = os.path.abspath('.')
if not os.path.exists(self.tmpDir):
os.mkdir(self.tmpDir)
# if not os.path.exists(os.path.join(tmpDir, self.inputFile)):
copy2(self.absInputFile, self.tmpDir)
os.chdir(self.tmpDir)
exten = self.ext[1:]
if self.ext == '.pdb':
tmpFile = open(self.inputFile, 'r')
else:
if exten == 'mol':
exten = 'mdl'
cmd = '%s -i %s -fi %s -o tmp -fo ac -pf y' % \
(self.acExe, self.inputFile, exten)
self.printDebug(cmd)
out = _getoutput(cmd)
if not out.isspace():
self.printDebug(out)
try:
tmpFile = open('tmp', 'r')
except:
rmtree(self.tmpDir)
raise
tmpData = tmpFile.readlines()
residues = set()
coords = {}
for line in tmpData:
if 'ATOM ' in line or 'HETATM' in line:
residues.add(line[17:20])
at = line[0:17]
cs = line[30:54]
if cs in coords:
coords[cs].append(at)
else:
coords[cs] = [at]
# self.printDebug(coords)
if len(residues) > 1:
self.printError("more than one residue detected '%s'" % str(residues))
self.printError("verify your input file '%s'. Aborting ..." % self.inputFile)
sys.exit(1)
dups = ""
shortd = ""
longd = ""
longSet = set()
id_ = 0
items = list(coords.items())
l = len(items)
for item in items:
id_ += 1
if len(item[1]) > 1: # if True means atoms with same coordinates
for i in item[1]:
dups += "%s %s\n" % (i, item[0])
# for i in xrange(0,len(data),f):
# fdata += (data[i:i+f])+' '
for id2 in range(id_, l):
item2 = items[id2]
c1 = list(map(float, [item[0][i:i + 8] for i in range(0, 24, 8)]))
c2 = list(map(float, [item2[0][i:i + 8] for i in range(0, 24, 8)]))
dist2 = self.distance(c1, c2)
if dist2 < minDist2:
dist = math.sqrt(dist2)
shortd += "%8.5f %s %s\n" % (dist, item[1], item2[1])
if dist2 < maxDist2: # and not longOK:
longSet.add(str(item[1]))
longSet.add(str(item2[1]))
if str(item[1]) not in longSet and l > 1:
longd += "%s\n" % item[1]
if dups:
self.printError("Atoms with same coordinates in '%s'!" % self.inputFile)
self.printQuoted(dups[:-1])
exit_ = True
if shortd:
self.printError("Atoms TOO close (< %s Ang.)" % minDist)
self.printQuoted("Dist (Ang.) Atoms\n" + shortd[:-1])
exit_ = True
if longd:
self.printError("Atoms TOO alone (> %s Ang.)" % maxDist)
self.printQuoted(longd[:-1])
exit_ = True
if exit_:
if self.force:
self.printWarn("You chose to proceed anyway with '-f' option. GOOD LUCK!")
else:
self.printError("Use '-f' option if you want to proceed anyway. Aborting ...")
rmtree(self.tmpDir)
sys.exit(1)
resname = list(residues)[0].strip()
newresname = resname
# To avoid resname likes: 001 (all numbers), 1e2 (sci number), ADD : reserved terms for leap
leapWords = ['_cmd_options_', '_types_', 'add', 'addAtomTypes', 'addIons',
'addIons2', 'addPath', 'addPdbAtomMap', 'addPdbResMap', 'alias',
'alignAxes', 'bond', 'bondByDistance', 'center', 'charge',
'check', 'clearPdbAtomMap', 'clearPdbResMap', 'clearVariables',
'combine', 'copy', 'createAtom', 'createParmset', 'createResidue',
'createUnit', 'crossLink', 'debugOff', 'debugOn', 'debugStatus',
'deleteBond', 'deleteOffLibEntry', 'deleteRestraint', 'desc',
'deSelect', 'displayPdbAtomMap', 'displayPdbResMap', 'edit',
'flip', 'groupSelectedAtoms', 'help', 'impose', 'list', 'listOff',
'loadAmberParams', 'loadAmberPrep', 'loadMol2', 'loadOff',
'loadPdb', 'loadPdbUsingSeq', 'logFile', 'matchVariables',
'measureGeom', 'quit', 'relax', 'remove', 'restrainAngle',
'restrainBond', 'restrainTorsion', 'saveAmberParm',
'saveAmberParmPert', 'saveAmberParmPol', 'saveAmberParmPolPert',
'saveAmberPrep', 'saveMol2', 'saveOff', 'saveOffParm', 'savePdb',
'scaleCharges', 'select', 'sequence', 'set', 'setBox', 'solvateBox',
'solvateCap', 'solvateDontClip', 'solvateOct', 'solvateShell',
'source', 'transform', 'translate', 'verbosity', 'zMatrix']
isLeapWord = False
for word in leapWords:
if resname.upper().startswith(word.upper()):
self.printDebug("Residue name is a reserved word: '%s'" % word.upper())
isLeapWord = True
try:
float(resname)
self.printDebug("Residue name is a 'number': '%s'" % resname)
isNumber = True
except ValueError:
isNumber = False
if resname[0].isdigit() or isNumber or isLeapWord:
newresname = 'R' + resname
if not resname.isalnum():
newresname = 'MOL'
if newresname != resname:
self.printWarn("In %s.lib, residue name will be '%s' instead of '%s' elsewhere"
% (self.acBaseName, newresname, resname))
self.resName = newresname
os.chdir(localDir)
self.printDebug("setResNameCheckCoords done")
def distance(self, c1, c2):
# print c1, c2
dist2 = (c1[0] - c2[0]) ** 2 + (c1[1] - c2[1]) ** 2 + (c1[0] - c2[0]) ** 2 + \
(c1[2] - c2[2]) ** 2
# dist2 = math.sqrt(dist2)
return dist2
def readMol2TotalCharge(self, mol2File):
"""Reads the charges in given mol2 file and returns the total
"""
charge = 0.0
ll = []
cmd = '%s -i %s -fi mol2 -o tmp -fo mol2 -c wc -cf tmp.crg -pf y' % \
(self.acExe, mol2File)
if self.debug:
self.printMess("Debugging...")
cmd = cmd.replace('-pf y', '-pf n')
self.printDebug(cmd)
log = _getoutput(cmd)
if os.path.exists('tmp.crg'):
tmpFile = open('tmp.crg', 'r')
tmpData = tmpFile.readlines()
for line in tmpData:
ll += line.split()
charge = sum(map(float, ll))
if not log.isspace() and self.debug:
self.printQuoted(log)
self.printDebug("readMol2TotalCharge: " + str(charge))
return charge
def execAntechamber(self, chargeType=None, atomType=None):
""" AmaberTools 1.3
To call Antechamber and execute it
Usage: antechamber -i input file name
-fi input file format
-o output file name
-fo output file format
-c charge method
-cf charge file name
-nc net molecular charge (int)
-a additional file name
-fa additional file format
-ao additional file operation
crd only read in coordinate
crg only read in charge
name only read in atom name
type only read in atom type
bond only read in bond type
-m multiplicity (2S+1), default is 1
-rn residue name, overrides input file, default is MOL
-rf residue toplogy file name in prep input file,
default is molecule.res
-ch check file name for gaussian, default is molecule
-ek mopac or sqm keyword, inside quotes
-gk gaussian keyword, inside quotes
-df am1-bcc flag, 2 - use sqm(default); 0 - use mopac
-at atom type, can be gaff (default), amber, bcc and sybyl
-du fix duplicate atom names: yes(y)[default] or no(n)
-j atom type and bond type prediction index, default is 4
0 no assignment
1 atom type
2 full bond types
3 part bond types
4 atom and full bond type
5 atom and part bond type
-s status information: 0(brief), 1(default) or 2(verbose)
-pf remove intermediate files: yes(y) or no(n)[default]
-i -o -fi and -fo must appear; others are optional
List of the File Formats
file format type abbre. index | file format type abbre. index
---------------------------------------------------------------
Antechamber ac 1 | Sybyl Mol2 mol2 2
PDB pdb 3 | Modified PDB mpdb 4
AMBER PREP (int) prepi 5 | AMBER PREP (car) prepc 6
Gaussian Z-Matrix gzmat 7 | Gaussian Cartesian gcrt 8
Mopac Internal mopint 9 | Mopac Cartesian mopcrt 10
Gaussian Output gout 11 | Mopac Output mopout 12
Alchemy alc 13 | CSD csd 14
MDL mdl 15 | Hyper hin 16
AMBER Restart rst 17 | Jaguar Cartesian jcrt 18
Jaguar Z-Matrix jzmat 19 | Jaguar Output jout 20
Divcon Input divcrt 21 | Divcon Output divout 22
Charmm charmm 23 | SQM Output sqmout 24
--------------------------------------------------------------
AMBER restart file can only be read in as additional file.
List of the Charge Methods
charge method abbre. index | charge method abbre. index
----------------------------------------------------------------
RESP resp 1 | AM1-BCC bcc 2
CM1 cm1 3 | CM2 cm2 4
ESP (Kollman) esp 5 | Mulliken mul 6
Gasteiger gas 7 | Read in charge rc 8
Write out charge wc 9 | Delete Charge dc 10
----------------------------------------------------------------
a """
global pid
self.printMess("Executing Antechamber...")
self.makeDir()
ct = chargeType or self.chargeType
at = atomType or self.atomType
if 'amber2' in at:
at = 'amber'
if ct == 'user':
ct = ''
else:
ct = '-c %s' % ct
exten = self.ext[1:]
if exten == 'mol':
exten = 'mdl'
cmd = '%s -i %s -fi %s -o %s -fo mol2 %s -nc %s -m %s -s 2 -df %i -at\
%s -pf y %s' % (self.acExe, self.inputFile, exten, self.acMol2FileName,
ct, self.chargeVal, self.multiplicity, self.qFlag, at,
self.ekFlag)
if self.debug:
self.printMess("Debugging...")
cmd = cmd.replace('-pf y', '-pf n')
self.printDebug(cmd)
if os.path.exists(self.acMol2FileName) and not self.force:
self.printMess("AC output file present... doing nothing")
else:
try:
os.remove(self.acMol2FileName)
except:
pass
signal.signal(signal.SIGALRM, self.signal_handler)
signal.alarm(self.timeTol)
p = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE)
pid = p.pid
out = str(p.communicate()[0].decode()) # p.stdout.read()
self.acLog = out
if os.path.exists(self.acMol2FileName):
self.printMess("* Antechamber OK *")
else:
self.printQuoted(self.acLog)
return True
def signal_handler(self, _signum, _frame): # , pid = 0):
global pid
pids = self.job_pids_family(pid)
self.printDebug("PID: %s, PIDS: %s" % (pid, pids))
self.printMess("Timed out! Process %s killed, max exec time (%ss) exceeded"
% (pids, self.timeTol))
# os.system('kill -15 %s' % pids)
for i in pids.split():
os.kill(int(i), 15)
raise Exception("Semi-QM taking too long to finish... aborting!")
def job_pids_family(self, jpid):
'''INTERNAL: Return all job processes (PIDs)'''
pid = repr(jpid)
dict_pids = {}
pids = [pid]
cmd = "ps -A -o uid,pid,ppid|grep %i" % os.getuid()
out = _getoutput(cmd).split('\n') # getoutput("ps -A -o uid,pid,ppid|grep %i" % os.getuid()).split('\n')
for item in out:
vec = item.split()
dict_pids[vec[2]] = vec[1]
while 1:
try:
pid = dict_pids[pid]
pids.append(pid)
except KeyError:
break
return ' '.join(pids)
def delOutputFiles(self):
delFiles = ['mopac.in', 'tleap.in', 'sleap.in', 'fixbo.log',
'addhs.log', 'ac_tmp_ot.mol2', 'frcmod.ac_tmp', 'fragment.mol2',
self.tmpDir] # , 'divcon.pdb', 'mopac.pdb', 'mopac.out'] #'leap.log'
self.printMess("Removing temporary files...")
for file_ in delFiles:
file_ = os.path.join(self.absHomeDir, file_)
if os.path.exists(file_):
if os.path.isdir(file_):
rmtree(file_)
else:
os.remove(file_)
def checkXyzAndTopFiles(self):
fileXyz = self.acXyzFileName
fileTop = self.acTopFileName
if os.path.exists(fileXyz) and os.path.exists(fileTop):
# self.acXyz = fileXyz
# self.acTop = fileTop
return True
return False
def execSleap(self):
global pid
self.makeDir()
if self.ext == '.mol2':
self.printWarn("Sleap doesn't work with mol2 files yet...")
return True
if self.chargeType != 'bcc':
self.printWarn("Sleap works only with bcc charge method")
return True
if self.atomType != 'gaff':
self.printWarn("Sleap works only with gaff atom type")
return True
sleapScpt = SLEAP_TEMPLATE % self.acParDict
fp = open('sleap.in', 'w')
fp.write(sleapScpt)
fp.close()
cmd = '%s -f sleap.in' % self.sleapExe
if self.checkXyzAndTopFiles() and not self.force:
self.printMess("Topologies files already present... doing nothing")
else:
try:
os.remove(self.acTopFileName)
os.remove(self.acXyzFileName)
except:
pass
self.printMess("Executing Sleap...")
self.printDebug(cmd)
p = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE)
pid = p.pid
signal.signal(signal.SIGALRM, self.signal_handler)
signal.alarm(self.timeTol)
out = str(p.communicate()[0].decode()) # p.stdout.read()
self.sleapLog = out
self.checkLeapLog(self.sleapLog)
if self.checkXyzAndTopFiles():
self.printMess(" * Sleap OK *")
else:
self.printQuoted(self.sleapLog)
return True
def execTleap(self):
fail = False
self.makeDir()
if self.ext == ".pdb":
self.printMess('... converting pdb input file to mol2 input file')
if self.convertPdbToMol2():
self.printError("convertPdbToMol2 failed")
# print self.chargeVal
if self.execAntechamber():
self.printError("Antechamber failed")
fail = True
# sys.exit(1)
if self.execParmchk():
self.printError("Parmchk failed")
fail = True
# sys.exit(1)
if fail:
return True
tleapScpt = TLEAP_TEMPLATE % self.acParDict
fp = open('tleap.in', 'w')
fp.write(tleapScpt)
fp.close()
cmd = '%s -f tleap.in' % self.tleapExe
if self.checkXyzAndTopFiles() and not self.force:
self.printMess("Topologies files already present... doing nothing")
else:
try:
os.remove(self.acTopFileName)
os.remove(self.acXyzFileName)
except:
pass
self.printMess("Executing Tleap...")
self.printDebug(cmd)
self.tleapLog = _getoutput(cmd)
self.checkLeapLog(self.tleapLog)
if self.checkXyzAndTopFiles():
self.printMess("* Tleap OK *")
else:
self.printQuoted(self.tleapLog)
return True
def checkLeapLog(self, log):
log = log.splitlines(True)
check = ''
block = False
for line in log:
# print "*"+line+"*"
if "Checking '" in line:
# check += line
block = True
if "Checking Unit." in line:
block = False
if block:
check += line
self.printQuoted(check[:-1])
def locateDat(self, aFile):
'''locate a file pertinent to $AMBERHOME/dat/leap/parm/'''
amberhome = os.environ.get('AMBERHOME')
if amberhome:
aFileF = os.path.join(amberhome, 'dat/leap/parm', aFile)
if os.path.exists(aFileF):
return aFileF
aFileF = os.path.join(os.path.dirname(self.acExe), '../dat/leap/parm', aFile)
if os.path.exists(aFileF):
return aFileF
return None
def execParmchk(self):
self.makeDir()
cmd = '%s -i %s -f mol2 -o %s' % (self.parmchkExe, self.acMol2FileName,
self.acFrcmodFileName)
if 'amber' in self.atomType:
gaffFile = self.locateDat(self.gaffDatfile)
parmfile = self.locateDat('parm10.dat')
frcmodffxxSB = self.locateDat('frcmod.ff14SB')
# frcmodparmbsc0 = self.locateDat('frcmod.parmbsc0')
parmGaffFile = parmMerge(parmfile, gaffFile)
parmGaffffxxSBFile = parmMerge(parmGaffFile, frcmodffxxSB, frcmod=True)
# parm99gaffff99SBparmbsc0File = parmMerge(parm99gaffff99SBFile, frcmodparmbsc0, frcmod = True)
# parm10file = self.locateDat('parm10.dat') # PARM99 + frcmod.ff99SB + frcmod.parmbsc0 in AmberTools 1.4
cmd += ' -p %s' % parmGaffffxxSBFile # Ignoring BSC0
elif 'gaff2' in self.atomType:
cmd += ' -s 2'
self.parmchkLog = _getoutput(cmd)
self.printDebug(cmd)
if os.path.exists(self.acFrcmodFileName):
check = self.checkFrcmod()
if check:
self.printWarn("Couldn't determine all parameters:")
self.printMess("From file '%s'\n" % self.acFrcmodFileName + check)
else:
self.printMess("* Parmchk OK *")
else:
self.printQuoted(self.parmchkLog)
return True
def checkFrcmod(self):
check = ""
frcmodContent = open(self.acFrcmodFileName, 'r').readlines()
for line in frcmodContent:
if "ATTN, need revision" in line:
check += line
return check
def convertPdbToMol2(self):
if self.ext == '.pdb':
if self.execBabel():
self.printError("convert pdb to mol2 via babel failed")
return True
def execBabel(self):
self.makeDir()
cmd = '%s -ipdb %s -omol2 %s.mol2' % (self.babelExe, self.inputFile,
self.baseName)
self.printDebug(cmd)
self.babelLog = _getoutput(cmd)
self.ext = '.mol2'
self.inputFile = self.baseName + self.ext
self.acParDict['ext'] = 'mol2'
if os.path.exists(self.inputFile):
self.printMess("* Babel OK *")
else:
self.printQuoted(self.babelLog)
return True
def makeDir(self):
os.chdir(self.rootDir)
self.absHomeDir = os.path.abspath(self.homeDir)
if not os.path.exists(self.homeDir):
os.mkdir(self.homeDir)
os.chdir(self.homeDir)
copy2(self.absInputFile, '.')
return True
def createACTopol(self):
"""
If successful, Amber Top and Xyz files will be generated
"""
# sleap = False
if self.engine == 'sleap':
if self.execSleap():
self.printError("Sleap failed")
self.printMess("... trying Tleap")
if self.execTleap():
self.printError("Tleap failed")
if self.engine == 'tleap':
if self.execTleap():
self.printError("Tleap failed")
if self.extOld == '.pdb':
self.printMess("... trying Sleap")
self.ext = self.extOld
self.inputFile = self.baseName + self.ext
if self.execSleap():
self.printError("Sleap failed")
if not self.debug:
self.delOutputFiles()
def createMolTopol(self):
"""
Create molTop obj
"""
self.topFileData = open(self.acTopFileName, 'r').readlines()
self.molTopol = MolTopol(self, verbose=self.verbose, debug=self.debug,
gmx4=self.gmx4, disam=self.disam, direct=self.direct,
is_sorted=self.sorted, chiral=self.chiral)
if self.outTopols:
if 'cns' in self.outTopols:
self.molTopol.writeCnsTopolFiles()
if 'gmx' in self.outTopols:
self.molTopol.writeGromacsTopolFiles()
if 'charmm' in self.outTopols:
self.writeCharmmTopolFiles()
self.pickleSave()
def pickleSave(self):
"""
To restore:
from acpype import *
#import cPickle as pickle
import pickle
o = pickle.load(open('DDD.pkl','rb'))
NB: It fails to restore with ipython in Mac (Linux OK)
"""
pklFile = self.baseName + ".pkl"
dumpFlag = False
if not os.path.exists(pklFile):
mess = "Writing pickle file %s" % pklFile
dumpFlag = True
elif self.force:
mess = "Overwriting pickle file %s" % pklFile
dumpFlag = True
else:
mess = "Pickle file %s already present... doing nothing" % pklFile
self.printMess(mess)
if dumpFlag:
with open(pklFile, "wb") as f: # for python 2.6 or higher
# f = open(pklFile, "wb")
if verList[0] == 3:
pickle.dump(self, f, protocol=2, fix_imports=True)
else:
pickle.dump(self, f, protocol=2)
def getFlagData(self, flag):
"""
For a given acFileTop flag, return a list of the data related
"""
block = False
tFlag = '%FLAG ' + flag
data = ''
if len(self.topFileData) == 0:
raise Exception("PRMTOP file empty?")
for rawLine in self.topFileData:
if '%COMMENT' in rawLine:
continue
line = rawLine.replace('\r', '').replace('\n', '')
if tFlag in line:
block = True
continue
if block and '%FLAG ' in line:
break
if block:
if '%FORMAT' in line:
line = line.strip().strip('%FORMAT()').split('.')[0]
for c in line:
if c.isalpha():
f = int(line.split(c)[1])
break
continue
data += line
# data need format
sdata = [data[i:i + f].strip() for i in range(0, len(data), f)]
if '+' and '.' in data and flag != 'RESIDUE_LABEL': # it's a float
ndata = list(map(float, sdata))
elif flag != 'RESIDUE_LABEL':
try: # try if it's integer
ndata = list(map(int, sdata))
except: # it's string
ndata = sdata
else:
ndata = sdata
if flag == 'AMBER_ATOM_TYPE':
nn = []
ll = set()
prefixed = False
for ii in ndata:
prefixed = True
if ii[0].isdigit():
ll.add(ii)
ii = 'A' + ii
nn.append(ii)
if prefixed and ll:
self.printDebug("GMX does not like atomtype starting with Digit")
self.printDebug("prefixing AtomType %s with 'A'." % list(ll))
ndata = nn
return ndata # a list
def getResidueLabel(self):
"""
Get a 3 capital letters code from acFileTop
Returns a list.
"""
residueLabel = self.getFlagData('RESIDUE_LABEL')
residueLabel = list(map(str, residueLabel))
if residueLabel[0] != residueLabel[0].upper():
self.printWarn("residue label '%s' in '%s' is not all UPPERCASE" %
(residueLabel[0], self.inputFile))
self.printWarn("this may raise problem with some applications like CNS")
self.residueLabel = residueLabel
def getCoords(self):
"""
For a given acFileXyz file, return a list of coords as:
[[x1,y1,z1],[x2,y2,z2], etc.]
"""
if len(self.xyzFileData) == 0:
raise Exception("INPCRD file empty?")
data = ''
for rawLine in self.xyzFileData[2:]:
line = rawLine.replace('\r', '').replace('\n', '')
data += line
l = len(data)
ndata = list(map(float, [data[i:i + 12] for i in range(0, l, 12)]))
gdata = []
for i in range(0, len(ndata), 3):
gdata.append([ndata[i], ndata[i + 1], ndata[i + 2]])
self.printDebug("getCoords done")
return gdata
def getAtoms(self):
"""
Set a list with all atoms objects build from dat in acFileTop
Set also if molTopol atom type system is gaff or amber
Set also list atomTypes
Set also resid
Set also molTopol total charge
"""
atomNameList = self.getFlagData('ATOM_NAME')
atomTypeNameList = self.getFlagData('AMBER_ATOM_TYPE')
self._atomTypeNameList = atomTypeNameList
massList = self.getFlagData('MASS')
chargeList = self.getFlagData('CHARGE')
# totalCharge = sum(chargeList)
# self.printDebug('charge to be balanced: total %13.10f' % (totalCharge/qConv))
resIds = self.getFlagData('RESIDUE_POINTER') + [0]
# to guess the resId of the last residue before ion or water
# for resTemp in self.residueLabel:
# if resTemp in ionOrWaterResNameList:
# lastSoluteResId = self.residueLabel.index(resTemp) - 1
# break
# print lastSoluteResId, self.residueLabel[lastSoluteResId]
# uniqAtomTypeId = self.getFlagData('ATOM_TYPE_INDEX') # for LJ
# balanceChargeList = self.balanceCharges(chargeList)
coords = self.getCoords()
ACOEFs, BCOEFs = self.getABCOEFs()
atoms = []
atomTypes = []
tmpList = [] # a list with unique atom types
totalCharge = 0.0
countRes = 0
id_ = 0
FirstNonSoluteId = None
for atomName in atomNameList:
if atomName != atomName.upper():
self.printDebug("atom name '%s' HAS to be all UPPERCASE... Applying this here." %
atomName)
atomName = atomName.upper()
atomTypeName = atomTypeNameList[id_]
if id_ + 1 == resIds[countRes]:
resid = countRes # self.residueLabel[countRes]
countRes += 1
resName = self.residueLabel[resid]
if resName in ionOrSolResNameList and not FirstNonSoluteId:
FirstNonSoluteId = id_
# print id_, resid, resName
mass = massList[id_]
# charge = balanceChargeList[id_]
charge = chargeList[id_]
chargeConverted = charge / qConv
totalCharge += charge
coord = coords[id_]
ACOEF = ACOEFs[id_]
BCOEF = BCOEFs[id_]
atomType = AtomType(atomTypeName, mass, ACOEF, BCOEF)
if atomTypeName not in tmpList:
tmpList.append(atomTypeName)
atomTypes.append(atomType)
atom = Atom(atomName, atomType, id_ + 1, resid, mass, chargeConverted, coord)
atoms.append(atom)
id_ += 1
balanceChargeList, balanceValue, balanceIds = self.balanceCharges(chargeList, FirstNonSoluteId)
for id_ in balanceIds:
atoms[id_].charge = balanceValue / qConv
# self.printDebug("atom ids and balanced charges: %s, %3f10" % (balanceIds, balanceValue/qConv))
if atomTypeName[0].islower():
self.atomTypeSystem = 'gaff'
else:
self.atomTypeSystem = 'amber'
self.printDebug('Balanced TotalCharge %13.10f' % float(sum(balanceChargeList) / qConv))
self.totalCharge = int(totalCharge)
self.atoms = atoms
self.atomTypes = atomTypes
self.pbc = None
if len(coords) == len(atoms) + 2 or len(coords) == len(atoms) * 2 + 2:
self.pbc = [coords[-2], coords[-1]]
self.printDebug("PBC = %s" % self.pbc)
self.printDebug("getAtoms done")
def getBonds(self):
uniqKbList = self.getFlagData('BOND_FORCE_CONSTANT')
uniqReqList = self.getFlagData('BOND_EQUIL_VALUE')
bondCodeHList = self.getFlagData('BONDS_INC_HYDROGEN')
bondCodeNonHList = self.getFlagData('BONDS_WITHOUT_HYDROGEN')
bondCodeList = bondCodeHList + bondCodeNonHList
bonds = []
for i in range(0, len(bondCodeList), 3):
idAtom1 = bondCodeList[i] // 3 # remember python starts with id 0
idAtom2 = bondCodeList[i + 1] // 3
bondTypeId = bondCodeList[i + 2] - 1
atom1 = self.atoms[idAtom1]
atom2 = self.atoms[idAtom2]
kb = uniqKbList[bondTypeId]
req = uniqReqList[bondTypeId]
atoms = [atom1, atom2]
bond = Bond(atoms, kb, req)
bonds.append(bond)
self.bonds = bonds
self.printDebug("getBonds done")
def getAngles(self):
uniqKtList = self.getFlagData('ANGLE_FORCE_CONSTANT')
uniqTeqList = self.getFlagData('ANGLE_EQUIL_VALUE')
# for list below, true atom number = index/3 + 1
angleCodeHList = self.getFlagData('ANGLES_INC_HYDROGEN')
angleCodeNonHList = self.getFlagData('ANGLES_WITHOUT_HYDROGEN')
angleCodeList = angleCodeHList + angleCodeNonHList
angles = []
for i in range(0, len(angleCodeList), 4):
idAtom1 = angleCodeList[i] // 3 # remember python starts with id 0
idAtom2 = angleCodeList[i + 1] // 3
idAtom3 = angleCodeList[i + 2] // 3
angleTypeId = angleCodeList[i + 3] - 1
atom1 = self.atoms[idAtom1]
atom2 = self.atoms[idAtom2]
atom3 = self.atoms[idAtom3]
kt = uniqKtList[angleTypeId]
teq = uniqTeqList[angleTypeId] # angle given in rad in prmtop
atoms = [atom1, atom2, atom3]
angle = Angle(atoms, kt, teq)
angles.append(angle)
self.angles = angles
self.printDebug("getAngles done")
def getDihedrals(self):
"""
Get dihedrals (proper and imp), condensed list of prop dih and
atomPairs
"""
uniqKpList = self.getFlagData('DIHEDRAL_FORCE_CONSTANT')
uniqPeriodList = self.getFlagData('DIHEDRAL_PERIODICITY')
uniqPhaseList = self.getFlagData('DIHEDRAL_PHASE')
# for list below, true atom number = abs(index)/3 + 1
dihCodeHList = self.getFlagData('DIHEDRALS_INC_HYDROGEN')
dihCodeNonHList = self.getFlagData('DIHEDRALS_WITHOUT_HYDROGEN')
dihCodeList = dihCodeHList + dihCodeNonHList
properDih = []
improperDih = []
condProperDih = [] # list of dihedrals condensed by the same quartet
# atomPairs = []
atomPairs = set()
for i in range(0, len(dihCodeList), 5):
idAtom1 = dihCodeList[i] // 3 # remember python starts with id 0
idAtom2 = dihCodeList[i + 1] // 3
# 3 and 4 indexes can be negative: if id3 < 0, end group interations
# in amber are to be ignored; if id4 < 0, dihedral is improper
idAtom3raw = dihCodeList[i + 2] // 3 # can be negative -> exclude from 1-4vdw
idAtom4raw = dihCodeList[i + 3] // 3 # can be negative -> Improper
idAtom3 = abs(idAtom3raw)
idAtom4 = abs(idAtom4raw)
dihTypeId = dihCodeList[i + 4] - 1
atom1 = self.atoms[idAtom1]
atom2 = self.atoms[idAtom2]
atom3 = self.atoms[idAtom3]
atom4 = self.atoms[idAtom4]
kPhi = uniqKpList[dihTypeId] # already divided by IDIVF
period = int(uniqPeriodList[dihTypeId]) # integer
phase = uniqPhaseList[dihTypeId] # angle given in rad in prmtop
if phase == kPhi == 0:
period = 0 # period is set to 0
atoms = [atom1, atom2, atom3, atom4]
dihedral = Dihedral(atoms, kPhi, period, phase)
if idAtom4raw > 0:
try:
atomsPrev = properDih[-1].atoms
except:
atomsPrev = []
properDih.append(dihedral)
if idAtom3raw < 0 and atomsPrev == atoms:
condProperDih[-1].append(dihedral)
else:
condProperDih.append([dihedral])
pair = (atom1, atom4)
# if atomPairs.count(pair) == 0 and idAtom3raw > 0:
if idAtom3raw > 0:
atomPairs.add(pair)
else:
improperDih.append(dihedral)
try:
atomPairs = sorted(atomPairs)
except:
pass
self.properDihedrals = properDih
self.improperDihedrals = improperDih
self.condensedProperDihedrals = condProperDih # [[],[],...]
self.atomPairs = atomPairs # set((atom1, atom2), ...)
self.printDebug("getDihedrals done")
def getChirals(self):
"""
Get chiral atoms, its 4 neighbours and improper dihedral angle
"""
self.chiralGroups = []
if self.obchiralExe:
# print (self.obchiralExe, os.getcwd())
cmd = '%s %s' % (self.obchiralExe, self.inputFile)
# print(cmd)
out = map(int, re.findall('Atom (\d+) Is', _getoutput(cmd)))
# print("*%s*" % out)
chiralGroups = []
for id_ in out:
atChi = self.atoms[id_ - 1]
quad = []
for bb in self.bonds:
bAts = bb.atoms[:]
if atChi in bAts:
bAts.remove(atChi)
quad.append(bAts[0])
if len(quad) != 4:
if self.chiral:
self.printWarn("Atom %s has less than 4 connections to 4 different atoms. It's NOT Chiral!" % atChi)
continue
v1, v2, v3, v4 = [x.coords for x in quad]
chiralGroups.append((atChi, quad, imprDihAngle(v1, v2, v3, v4)))
self.chiralGroups = chiralGroups
def sortAtomsForGromacs(self):
"""
Re-sort atoms for gromacs, which expects all hydrogens to immediately
follow the heavy atom they are bonded to and belong to the same charge
group.
Currently, atom mass < 1.2 is taken to denote a proton. This behavior
may be changed by modifying the 'is_hydrogen' function within.
JDC 2011-02-03
"""
# Build dictionary of bonded atoms.
bonded_atoms = dict()
for atom in self.atoms:
bonded_atoms[atom] = list()
for bond in self.bonds:
[atom1, atom2] = bond.atoms
bonded_atoms[atom1].append(atom2)
bonded_atoms[atom2].append(atom1)
# Define hydrogen and heavy atom classes.
def is_hydrogen(atom):
return (atom.mass < 1.2)
def is_heavy(atom):
return not is_hydrogen(atom)
# Build list of sorted atoms, assigning charge groups by heavy atom.
sorted_atoms = list()
cgnr = 1 # charge group number: each heavy atoms is assigned its own charge group
# First pass: add heavy atoms, followed by the hydrogens bonded to them.
for atom in self.atoms:
if is_heavy(atom):
# Append heavy atom.
atom.cgnr = cgnr
sorted_atoms.append(atom)
# Append all hydrogens.
for bonded_atom in bonded_atoms[atom]:
if is_hydrogen(bonded_atom) and not (bonded_atom in sorted_atoms):
# Append bonded hydrogen.
bonded_atom.cgnr = cgnr
sorted_atoms.append(bonded_atom)
cgnr += 1
# Second pass: Add any remaining atoms.
if len(sorted_atoms) < len(self.atoms):
for atom in self.atoms:
if not (atom in sorted_atoms):
atom.cgnr = cgnr
sorted_atoms.append(atom)
cgnr += 1
# Replace current list of atoms with sorted list.
self.atoms = sorted_atoms
# Renumber atoms in sorted list, starting from 1.
for (index, atom) in enumerate(self.atoms):
atom.id = index + 1
return
def setAtomPairs(self):
"""
Set a list of pair of atoms pertinent to interaction 1-4 for vdw.
WRONG: Deprecated
"""
atomPairs = []
for item in self.condensedProperDihedrals:
dih = item[0]
atom1 = dih.atoms[0]
atom2 = dih.atoms[3]
pair = [atom1, atom2]
if atomPairs.count(pair) == 0:
atomPairs.append(pair)
self.atomPairs = atomPairs # [[atom1, atom2], ...]
self.printDebug("atomPairs done")
def getExcludedAtoms(self):
"""
Returns a list of atoms with a list of its excluded atoms up to 3rd
neighbour.
It's implicitly indexed, i.e., a sequence of atoms in position n in
the excludedAtomsList corresponds to atom n (self.atoms) and so on.
NOT USED
"""
excludedAtomsIdList = self.getFlagData('EXCLUDED_ATOMS_LIST')
numberExcludedAtoms = self.getFlagData('NUMBER_EXCLUDED_ATOMS')
atoms = self.atoms
interval = 0
excludedAtomsList = []
for number in numberExcludedAtoms:
temp = excludedAtomsIdList[interval:interval + number]
if temp == [0]:
excludedAtomsList.append([])
else:
excludedAtomsList.append([atoms[a - 1] for a in temp])
interval += number
self.excludedAtoms = excludedAtomsList
self.printDebug("getExcludedAtoms")
def balanceCharges(self, chargeList, FirstNonSoluteId=None):
"""
Note that python is very annoying about floating points.
Even after balance, there will always be some residue of order e-12
to e-16, which is believed to vanished once one writes a topology
file, say, for CNS or GMX, where floats are represented with 4 or 5
maximum decimals.
"""
limIds = []
# self.printDebug(chargeList)
total = sum(chargeList)
totalConverted = total / qConv
self.printDebug('charge to be balanced: total %13.10f' % (totalConverted))
maxVal = max(chargeList[:FirstNonSoluteId])
minVal = min(chargeList[:FirstNonSoluteId])
if abs(maxVal) >= abs(minVal):
lim = maxVal
else:
lim = minVal
nLims = chargeList.count(lim)
# limId = chargeList.index(lim)
diff = totalConverted - round(totalConverted)
fix = lim - diff * qConv / nLims
id_ = 0
for c in chargeList:
if c == lim:
limIds.append(id_)
chargeList[id_] = fix
id_ += 1
# self.printDebug(chargeList)
self.printDebug("balanceCharges done")
return chargeList, fix, limIds
def getABCOEFs(self):
uniqAtomTypeIdList = self.getFlagData('ATOM_TYPE_INDEX')
nonBonIdList = self.getFlagData('NONBONDED_PARM_INDEX')
rawACOEFs = self.getFlagData('LENNARD_JONES_ACOEF')
rawBCOEFs = self.getFlagData('LENNARD_JONES_BCOEF')
# print nonBonIdList, len(nonBonIdList), rawACOEFs, len(rawACOEFs)
ACOEFs = []
BCOEFs = []
ntypes = max(uniqAtomTypeIdList)
# id_ = 0
# for atName in self._atomTypeNameList:
for id_ in range(len(self._atomTypeNameList)):
# id_ = self._atomTypeNameList.index(atName)
atomTypeId = uniqAtomTypeIdList[id_]
index = ntypes * (atomTypeId - 1) + atomTypeId
nonBondId = nonBonIdList[index - 1]
# print "*****", index, ntypes, atName, id_, atomTypeId, nonBondId
ACOEFs.append(rawACOEFs[nonBondId - 1])
BCOEFs.append(rawBCOEFs[nonBondId - 1])
# id_ += 1
# print ACOEFs
self.printDebug("getABCOEFs done")
return ACOEFs, BCOEFs
def setProperDihedralsCoef(self):
"""
It takes self.condensedProperDihedrals and returns
self.properDihedralsCoefRB, a reduced list of quartet atoms + RB.
Coeficients ready for GMX (multiplied by 4.184)
self.properDihedralsCoefRB = [ [atom1,..., atom4], C[0:5] ]
For proper dihedrals: a quartet of atoms may appear with more than
one set of parameters and to convert to GMX they are treated as RBs.
The resulting coefs calculated here may look slighted different from
the ones calculated by amb2gmx.pl because python is taken full float
number from prmtop and not rounded numbers from rdparm.out as
amb2gmx.pl does.
"""
properDihedralsCoefRB = []
properDihedralsAlphaGamma = []
properDihedralsGmx45 = []
for item in self.condensedProperDihedrals:
V = 6 * [0.0]
C = 6 * [0.0]
for dih in item:
period = dih.period # Pn
kPhi = dih.kPhi # in rad
phaseRaw = dih.phase * radPi # in degree
phase = int(phaseRaw) # in degree
if period > 4 and self.gmx4:
self.printError("Likely trying to convert ILDN to RB, DO NOT use option '-z'")
sys.exit(1)
if phase in [0, 180]:
properDihedralsGmx45.append([item[0].atoms, phaseRaw, kPhi, period])
if self.gmx4:
if kPhi > 0:
V[period] = 2 * kPhi * cal
if period == 1:
C[0] += 0.5 * V[period]
if phase == 0:
C[1] -= 0.5 * V[period]
else:
C[1] += 0.5 * V[period]
elif period == 2:
if phase == 180:
C[0] += V[period]
C[2] -= V[period]
else:
C[2] += V[period]
elif period == 3:
C[0] += 0.5 * V[period]
if phase == 0:
C[1] += 1.5 * V[period]
C[3] -= 2 * V[period]
else:
C[1] -= 1.5 * V[period]
C[3] += 2 * V[period]
elif period == 4:
if phase == 180:
C[2] += 4 * V[period]
C[4] -= 4 * V[period]
else:
C[0] += V[period]
C[2] -= 4 * V[period]
C[4] += 4 * V[period]
else:
properDihedralsAlphaGamma.append([item[0].atoms, phaseRaw, kPhi, period])
# print phaseRaw, kPhi, period
if phase in [0, 180]:
properDihedralsCoefRB.append([item[0].atoms, C])
# print properDihedralsCoefRB
# print properDihedralsAlphaGamma
self.printDebug("setProperDihedralsCoef done")
self.properDihedralsCoefRB = properDihedralsCoefRB
self.properDihedralsAlphaGamma = properDihedralsAlphaGamma
self.properDihedralsGmx45 = properDihedralsGmx45
def writeCharmmTopolFiles(self):
self.printMess("Writing CHARMM files\n")
# self.makeDir()
at = self.atomType
self.getResidueLabel()
res = self.resName # self.residueLabel[0]
# print res, self.residueLabel, type(self.residueLabel)
cmd = '%s -i %s -fi mol2 -o %s -fo charmm -s 2 -at %s \
-pf y -rn %s' % (self.acExe, self.acMol2FileName, self.charmmBase,
at, res)
if self.debug:
cmd = cmd.replace('-pf y', '-pf n')
self.printDebug(cmd)
_log = _getoutput(cmd)
def writePdb(self, file_):
"""
Write a new PDB file_ with the atom names defined by Antechamber
Input: file_ path string
The format generated here use is slightly different from
http://www.wwpdb.org/documentation/format23/sect9.html respected to
atom name
"""
# TODO: assuming only one residue ('1')
pdbFile = open(file_, 'w')
fbase = os.path.basename(file_)
pdbFile.write("REMARK " + head % (fbase, date))
id_ = 1
for atom in self.atoms:
# id_ = self.atoms.index(atom) + 1
aName = atom.atomName
if len(aName) == 2:
aName = ' %s ' % aName
elif len(aName) == 1:
aName = ' %s ' % aName
for l in aName:
if l.isalpha():
s = l
break
rName = self.residueLabel[0]
x = atom.coords[0]
y = atom.coords[1]
z = atom.coords[2]
line = "%-6s%5d %4s %3s Z%4d%s%8.3f%8.3f%8.3f%6.2f%6.2f%s%2s\n" % \
('ATOM', id_, aName, rName, 1, 4 * ' ', x, y, z, 1.0, 0.0, 10 * ' ', s)
pdbFile.write(line)
id_ += 1
pdbFile.write('END\n')
def writeGromacsTopolFiles(self, amb2gmx=False):
"""
# from ~/Programmes/amber10/dat/leap/parm/gaff.dat
#atom type atomic mass atomic polarizability comments
ca 12.01 0.360 Sp2 C in pure aromatic systems
ha 1.008 0.135 H bonded to aromatic carbon
#bonded atoms harmonic force kcal/mol/A^2 eq. dist. Ang. comments
ca-ha 344.3* 1.087** SOURCE3 1496 0.0024 0.0045
* for gmx: 344.3 * 4.184 * 100 * 2 = 288110 kJ/mol/nm^2 (why factor 2?)
** convert Ang to nm ( div by 10) for gmx: 1.087 A = 0.1087 nm
# CA HA 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; PHE,TRP,TYR (from ffamber99bon.itp)
# CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR (from parm99.dat)
# angle HF kcal/mol/rad^2 eq angle degrees comments
ca-ca-ha 48.5* 120.01 SOURCE3 2980 0.1509 0.2511
* to convert to gmx: 48.5 * 4.184 * 2 = 405.848 kJ/mol/rad^2 (why factor 2?)
# CA CA HA 1 120.000 418.400 ; new99 (from ffamber99bon.itp)
# CA-CA-HA 50.0 120.00 (from parm99.dat)
# dihedral idivf barrier hight/2 kcal/mol phase degrees periodicity comments
X -ca-ca-X 4 14.500* 180.000 2.000 intrpol.bsd.on C6H6
* to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, not in topolbuild, why?) = 30.334 or 15.167 kJ/mol
# X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 (from parm99.dat)
# X CA CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6
;propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet (from ffamber99bon.itp)
# impr. dihedral barrier hight/2 phase degrees periodicity comments
X -X -ca-ha 1.1* 180. 2. bsd.on C6H6 nmodes
* to convert to gmx: 1.1 * 4.184 = 4.6024 kJ/mol/rad^2
# X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes (from parm99.dat)
# X X CA HA 1 180.00 4.60240 2 ; bsd.on C6H6 nmodes
;impropers treated as propers in GROMACS to use correct AMBER analytical function (from ffamber99bon.itp)
# 6-12 parms sigma = 2 * r * 2^(-1/6) epsilon
# atomtype radius Ang. pot. well depth kcal/mol comments
ha 1.4590* 0.0150** Spellmeyer
ca 1.9080 0.0860 OPLS
* to convert to gmx:
sigma = 1.4590 * 2^(-1/6) * 2 = 2 * 1.29982 Ang. = 2 * 0.129982 nm = 1.4590 * 2^(5/6)/10 = 0.259964 nm
** to convert to gmx: 0.0150 * 4.184 = 0.06276 kJ/mol
# amber99_3 CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 (from ffamber99nb.itp)
# amber99_22 HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 (from ffamber99nb.itp)
# C* 1.9080 0.0860 Spellmeyer
# HA 1.4590 0.0150 Spellmeyer (from parm99.dat)
# to convert r and epsilon to ACOEF and BCOEF
# ACOEF = sqrt(e1*e2) * (r1 + r2)^12 ; BCOEF = 2 * sqrt(e1*e2) * (r1 + r2)^6 = 2 * ACOEF/(r1+r2)^6
# to convert ACOEF and BCOEF to r and epsilon
# r = 0.5 * (2*ACOEF/BCOEF)^(1/6); ep = BCOEF^2/(4*ACOEF)
# to convert ACOEF and BCOEF to sigma and epsilon (GMX)
# sigma = (ACOEF/BCOEF)^(1/6) * 0.1 ; epsilon = 4.184 * BCOEF^2/(4*ACOEF)
# ca ca 819971.66 531.10
# ca ha 76245.15 104.66
# ha ha 5716.30 18.52
For proper dihedrals: a quartet of atoms may appear with more than
one set of parameters and to convert to GMX they are treated as RBs;
use the algorithm:
for(my $j=$i;$j<=$lines;$j++){
my $period = $pn{$j};
if($pk{$j}>0) {
$V[$period] = 2*$pk{$j}*$cal;
}
# assign V values to C values as predefined #
if($period==1){
$C[0]+=0.5*$V[$period];
if($phase{$j}==0){
$C[1]-=0.5*$V[$period];
}else{
$C[1]+=0.5*$V[$period];
}
}elsif($period==2){
if(($phase{$j}==180)||($phase{$j}==3.14)){
$C[0]+=$V[$period];
$C[2]-=$V[$period];
}else{
$C[2]+=$V[$period];
}
}elsif($period==3){
$C[0]+=0.5*$V[$period];
if($phase{$j}==0){
$C[1]+=1.5*$V[$period];
$C[3]-=2*$V[$period];
}else{
$C[1]-=1.5*$V[$period];
$C[3]+=2*$V[$period];
}
}elsif($period==4){
if(($phase{$j}==180)||($phase{$j}==3.14)){
$C[2]+=4*$V[$period];
$C[4]-=4*$V[$period];
}else{
$C[0]+=$V[$period];
$C[2]-=4*$V[$period];
$C[4]+=4*$V[$period];
}
}
}
"""
self.printMess("Writing GROMACS files\n")
self.setAtomType4Gromacs()
self.writeGroFile()
self.writeGromacsTop(amb2gmx=amb2gmx)
self.writeMdpFiles()
def setAtomType4Gromacs(self):
"""Atom types names in Gromacs TOP file are not case sensitive;
this routine will append a '_' to lower case atom type.
E.g.: CA and ca -> CA and ca_
"""
if self.disam:
self.printMess("Disambiguating lower and uppercase atomtypes in GMX top file.\n")
self.atomTypesGromacs = self.atomTypes
self.atomsGromacs = self.atoms
return
atNames = [at.atomTypeName for at in self.atomTypes]
# print atNames
delAtomTypes = []
modAtomTypes = []
atomTypesGromacs = []
dictAtomTypes = {}
for at in self.atomTypes:
atName = at.atomTypeName
dictAtomTypes[atName] = at
if atName.islower() and atName.upper() in atNames:
# print atName, atName.upper()
atUpper = self.atomTypes[atNames.index(atName.upper())]
# print at.atomTypeName,at.mass, at.ACOEF, at.BCOEF
# print atUpper.atomTypeName, atUpper.mass, atUpper.ACOEF, atUpper.BCOEF
if at.ACOEF is atUpper.ACOEF and at.BCOEF is at.BCOEF:
delAtomTypes.append(atName)
else:
newAtName = atName + '_'
modAtomTypes.append(atName)
atomType = AtomType(newAtName, at.mass, at.ACOEF, at.BCOEF)
atomTypesGromacs.append(atomType)
dictAtomTypes[newAtName] = atomType
else:
atomTypesGromacs.append(at)
atomsGromacs = []
for a in self.atoms:
atName = a.atomType.atomTypeName
if atName in delAtomTypes:
atom = Atom(a.atomName, dictAtomTypes[atName.upper()], a.id,
a.resid, a.mass, a.charge, a.coords)
atom.cgnr = a.cgnr
atomsGromacs.append(atom)
elif atName in modAtomTypes:
atom = Atom(a.atomName, dictAtomTypes[atName + '_'], a.id,
a.resid, a.mass, a.charge, a.coords)
atom.cgnr = a.cgnr
atomsGromacs.append(atom)
else:
atomsGromacs.append(a)
self.atomTypesGromacs = atomTypesGromacs
self.atomsGromacs = atomsGromacs
# print [i.atomTypeName for i in atomTypesGromacs]
# print modAtomTypes
# print delAtomTypes
def writeGromacsTop(self, amb2gmx=False):
if self.atomTypeSystem == 'amber':
d2opls = dictAtomTypeAmb2OplsGmxCode
else:
d2opls = dictAtomTypeGaff2OplsGmxCode
topText = []
itpText = []
oitpText = []
otopText = []
top = self.baseName + '_GMX.top'
itp = self.baseName + '_GMX.itp'
otop = self.baseName + '_GMX_OPLS.top'
oitp = self.baseName + '_GMX_OPLS.itp'
headDefault = \
"""
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
"""
headItp = \
"""
; Include %s topology
#include "%s"
"""
headOpls = \
"""
; Include forcefield parameters
#include "ffoplsaa.itp"
"""
headSystem = \
"""
[ system ]
%s
"""
headMols = \
"""
[ molecules ]
; Compound nmols
"""
headAtomtypes = \
"""
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
"""
headAtomtypesOpls = \
"""
; For OPLS atomtypes manual fine tuning
; AC_at:OPLS_at:OPLScode: Possible_Aternatives (see ffoplsaa.atp and ffoplsaanb.itp)
"""
headMoleculetype = \
"""
[ moleculetype ]
;name nrexcl
%-16s 3
"""
headAtoms = \
"""
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
"""
headBonds = \
"""
[ bonds ]
; ai aj funct r k
"""
headPairs = \
"""
[ pairs ]
; ai aj funct
"""
headAngles = \
"""
[ angles ]
; ai aj ak funct theta cth
"""
headProDih = \
"""
[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet
; i j k l func C0 C1 C2 C3 C4 C5
"""
headProDihAlphaGamma = """; treated as usual propers in GROMACS since Phase angle diff from 0 or 180 degrees
; i j k l func phase kd pn
"""
headProDihGmx45 = \
"""
[ dihedrals ] ; propers
; for gromacs 4.5 or higher, using funct 9
; i j k l func phase kd pn
"""
headImpDih = \
"""
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
"""
_headTopWaterTip3p = \
"""
[ bondtypes ]
; i j func b0 kb
OW HW 1 0.09572 462750.4 ; TIP3P water
HW HW 1 0.15139 462750.4 ; TIP3P water
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 104.520 836.800 ; TIP3P water
HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds)
"""
_headTopWaterSpce = \
"""
[ bondtypes ]
; i j func b0 kb
OW HW 1 0.1 462750.4 ; SPCE water
HW HW 1 0.1633 462750.4 ; SPCE water
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 109.47 836.800 ; SPCE water
HW HW OW 1 125.265 0.000 ; SPCE water
"""
# NOTE: headTopWaterTip3p and headTopWaterSpce actually do NOTHING
headNa = \
"""
[ moleculetype ]
; molname nrexcl
NA+ 1
[ atoms ]
; id_ at type res nr residu name at name cg nr charge mass
1 IP 1 NA+ NA+ 1 1 22.9898
"""
headCl = \
"""
[ moleculetype ]
; molname nrexcl
CL- 1
[ atoms ]
; id_ at type res nr residu name at name cg nr charge mass
1 IM 1 CL- CL- 1 -1 35.45300
"""
headK = \
"""
[ moleculetype ]
; molname nrexcl
K+ 1
[ atoms ]
; id_ at type res nr residu name at name cg nr charge mass
1 K 1 K+ K+ 1 1 39.100
"""
headWaterTip3p = \
"""
[ moleculetype ]
; molname nrexcl ; TIP3P model
WAT 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 WAT O 1 -0.834 16.00000
2 HW 1 WAT H1 1 0.417 1.00800
3 HW 1 WAT H2 1 0.417 1.00800
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 462750.4 0.09572 462750.4
1 3 1 0.09572 462750.4 0.09572 462750.4
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.520 836.800 104.520 836.800
#else
[ settles ]
; i j funct length
1 1 0.09572 0.15139
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
"""
headWaterSpce = \
"""
[ moleculetype ]
; molname nrexcl ; SPCE model
WAT 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 WAT O 1 -0.8476 15.99940
2 HW 1 WAT H1 1 0.4238 1.00800
3 HW 1 WAT H2 1 0.4238 1.00800
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 462750.4 0.1 462750.4
1 3 1 0.1 462750.4 0.1 462750.4
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 836.800 109.47 836.800
#else
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
"""
if self.direct and amb2gmx:
self.printMess("Converting directly from AMBER to GROMACS.\n")
# Dict of ions dealt by acpype emulating amb2gmx
ionsDict = {'Na+': headNa, 'Cl-': headCl, 'K+': headK}
ionsSorted = []
# NOTE: headWaterTip3p and headWaterSpce actually do the real thing
# so, skipping headTopWaterTip3p and headWaterTip3p
# headTopWater = headTopWaterTip3p
headWater = headWaterTip3p
nWat = 0
# topFile.write("; " + head % (top, date))
topText.append("; " + head % (top, date))
otopText.append("; " + head % (otop, date))
# topFile.write(headDefault)
topText.append(headDefault)
nSolute = 0
if not amb2gmx:
topText.append(headItp % (itp, itp))
otopText.append(headOpls)
otopText.append(headItp % (itp, itp))
itpText.append("; " + head % (itp, date))
oitpText.append("; " + head % (oitp, date))
self.printDebug("atomTypes %i" % len(self.atomTypesGromacs))
temp = []
otemp = []
for aType in self.atomTypesGromacs:
aTypeName = aType.atomTypeName
oaCode = d2opls.get(aTypeName, ['x', '0'])[:-1]
aTypeNameOpls = oplsCode2AtomTypeDict.get(oaCode[0], 'x')
A = aType.ACOEF
B = aType.BCOEF
# one cannot infer sigma or epsilon for B = 0, assuming 0 for them
if B == 0.0:
sigma, epsilon, r0, epAmber = 0, 0, 0, 0
else:
r0 = 0.5 * math.pow((2 * A / B), (1.0 / 6))
epAmber = 0.25 * B * B / A
sigma = 0.1 * math.pow((A / B), (1.0 / 6))
epsilon = cal * epAmber
if aTypeName == 'OW':
if A == 629362.166 and B == 625.267765:
# headTopWater = headTopWaterSpce
headWater = headWaterSpce
# OW 629362.166 625.267765 spce
# OW 581935.564 594.825035 tip3p
# print aTypeName, A, B
line = " %-8s %-11s %3.5f %3.5f A %13.5e %13.5e" % \
(aTypeName, aTypeName, 0.0, 0.0, sigma, epsilon) + \
" ; %4.2f %1.4f\n" % (r0, epAmber)
oline = "; %s:%s:opls_%s: %s\n" % (aTypeName, aTypeNameOpls, oaCode[0], repr(oaCode[1:]))
# tmpFile.write(line)
temp.append(line)
otemp.append(oline)
if amb2gmx:
topText.append(headAtomtypes)
topText += temp
nWat = self.residueLabel.count('WAT')
for ion in ionsDict:
nIon = self.residueLabel.count(ion)
if nIon > 0:
idIon = self.residueLabel.index(ion)
ionsSorted.append((idIon, nIon, ion))
ionsSorted.sort()
else:
itpText.append(headAtomtypes)
itpText += temp
oitpText.append(headAtomtypesOpls)
oitpText += otemp
self.printDebug("GMX atomtypes done")
if len(self.atoms) > 3 * nWat + sum([x[1] for x in ionsSorted]):
nSolute = 1
if nWat:
# topText.append(headTopWater)
self.printDebug("type of water '%s'" % headWater[43:48].strip())
if nSolute:
if amb2gmx:
topText.append(headMoleculetype % self.baseName)
else:
itpText.append(headMoleculetype % self.baseName)
oitpText.append(headMoleculetype % self.baseName)
self.printDebug("atoms %i" % len(self.atoms))
qtot = 0.0
count = 1
temp = []
otemp = []
id2oplsATDict = {}
for atom in self.atomsGromacs:
resid = atom.resid
resname = self.residueLabel[resid]
if not self.direct:
if resname in list(ionsDict.keys()) + ['WAT']:
break
aName = atom.atomName
aType = atom.atomType.atomTypeName
oItem = d2opls.get(aType, ['x', 0])
oplsAtName = oplsCode2AtomTypeDict.get(oItem[0], 'x')
id_ = atom.id
id2oplsATDict[id_] = oplsAtName
oaCode = 'opls_' + oItem[0]
cgnr = id_
if self.sorted:
cgnr = atom.cgnr # JDC
charge = atom.charge
mass = atom.mass
omass = float(oItem[-1])
qtot += charge
resnr = resid + 1
line = "%6d %4s %5d %5s %5s %4d %12.6f %12.5f ; qtot %1.3f\n" % \
(id_, aType, resnr, resname, aName, cgnr, charge, mass, qtot) # JDC
oline = "%6d %4s %5d %5s %5s %4d %12.6f %12.5f ; qtot % 3.3f %-4s\n" % \
(id_, oaCode, resnr, resname, aName, cgnr, charge, omass, qtot, oplsAtName) # JDC
count += 1
temp.append(line)
otemp.append(oline)
if temp:
if amb2gmx:
topText.append(headAtoms)
topText += temp
else:
itpText.append(headAtoms)
itpText += temp
oitpText.append(headAtoms)
oitpText += otemp
self.printDebug("GMX atoms done")
# remove bond of water
self.printDebug("bonds %i" % len(self.bonds))
temp = []
otemp = []
for bond in self.bonds:
res1 = self.residueLabel[bond.atoms[0].resid]
res2 = self.residueLabel[bond.atoms[0].resid]
if 'WAT' in [res1, res2]:
continue
a1Name = bond.atoms[0].atomName
a2Name = bond.atoms[1].atomName
id1 = bond.atoms[0].id
id2 = bond.atoms[1].id
oat1 = id2oplsATDict.get(id1)
oat2 = id2oplsATDict.get(id2)
line = "%6i %6i %3i %13.4e %13.4e ; %6s - %-6s\n" % (id1, id2, 1,
bond.rEq * 0.1, bond.kBond * 200 * cal, a1Name, a2Name)
oline = "%6i %6i %3i ; %13.4e %13.4e ; %6s - %-6s %6s - %-6s\n" % \
(id1, id2, 1, bond.rEq * 0.1, bond.kBond * 200 * cal, a1Name,
a2Name, oat1, oat2)
temp.append(line)
otemp.append(oline)
temp.sort()
otemp.sort()
if temp:
if amb2gmx:
topText.append(headBonds)
topText += temp
else:
itpText.append(headBonds)
itpText += temp
oitpText.append(headBonds)
oitpText += otemp
self.printDebug("GMX bonds done")
self.printDebug("atomPairs %i" % len(self.atomPairs))
temp = []
for pair in self.atomPairs:
# if not printed:
# tmpFile.write(headPairs)
# printed = True
a1Name = pair[0].atomName
a2Name = pair[1].atomName
id1 = pair[0].id
id2 = pair[1].id
# id1 = self.atoms.index(pair[0]) + 1
# id2 = self.atoms.index(pair[1]) + 1
line = "%6i %6i %6i ; %6s - %-6s\n" % (id1, id2, 1, a1Name,
a2Name)
temp.append(line)
temp.sort()
if temp:
if amb2gmx:
topText.append(headPairs)
topText += temp
else:
itpText.append(headPairs)
itpText += temp
oitpText.append(headPairs)
oitpText += temp
self.printDebug("GMX pairs done")
self.printDebug("angles %i" % len(self.angles))
temp = []
otemp = []
for angle in self.angles:
a1 = angle.atoms[0].atomName
a2 = angle.atoms[1].atomName
a3 = angle.atoms[2].atomName
id1 = angle.atoms[0].id
id2 = angle.atoms[1].id
id3 = angle.atoms[2].id
oat1 = id2oplsATDict.get(id1)
oat2 = id2oplsATDict.get(id2)
oat3 = id2oplsATDict.get(id3)
line = "%6i %6i %6i %6i %13.4e %13.4e ; %6s - %-6s - %-6s\n" % (id1, id2,
id3, 1, angle.thetaEq * radPi, 2 * cal * angle.kTheta, a1, a2, a3)
oline = "%6i %6i %6i %6i ; %13.4e %13.4e ; %6s - %-4s - %-6s %4s - %+4s - %-4s\n" % \
(id1, id2, id3, 1, angle.thetaEq * radPi, 2 * cal * angle.kTheta,
a1, a2, a3, oat1, oat2, oat3)
temp.append(line)
otemp.append(oline)
temp.sort()
otemp.sort()
if temp:
if amb2gmx:
topText.append(headAngles)
topText += temp
else:
itpText.append(headAngles)
itpText += temp
oitpText.append(headAngles)
oitpText += otemp
self.printDebug("GMX angles done")
self.setProperDihedralsCoef()
self.printDebug("properDihedralsCoefRB %i" % len(self.properDihedralsCoefRB))
self.printDebug("properDihedralsAlphaGamma %i" % len(self.properDihedralsAlphaGamma))
self.printDebug("properDihedralsGmx45 %i" % len(self.properDihedralsGmx45))
temp = []
otemp = []
if self.gmx4:
self.printMess("Writing RB dihedrals for old GMX 4.\n")
for dih in self.properDihedralsCoefRB:
a1 = dih[0][0].atomName
a2 = dih[0][1].atomName
a3 = dih[0][2].atomName
a4 = dih[0][3].atomName
id1 = dih[0][0].id
id2 = dih[0][1].id
id3 = dih[0][2].id
id4 = dih[0][3].id
oat1 = id2oplsATDict.get(id1)
oat2 = id2oplsATDict.get(id2)
oat3 = id2oplsATDict.get(id3)
oat4 = id2oplsATDict.get(id4)
c0, c1, c2, c3, c4, c5 = dih[1]
line = \
"%6i %6i %6i %6i %6i %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f" % \
(id1, id2, id3, id4, 3, c0, c1, c2, c3, c4, c5) \
+ " ; %6s-%6s-%6s-%6s\n" % (a1, a2, a3, a4)
oline = \
"%6i %6i %6i %6i %6i ; %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f" % \
(id1, id2, id3, id4, 3, c0, c1, c2, c3, c4, c5) \
+ " ; %6s-%6s-%6s-%6s %4s-%4s-%4s-%4s\n" % (a1, a2, a3, a4, oat1, oat2, oat3, oat4)
temp.append(line)
otemp.append(oline)
temp.sort()
otemp.sort()
if temp:
if amb2gmx:
topText.append(headProDih)
topText += temp
else:
itpText.append(headProDih)
itpText += temp
oitpText.append(headProDih)
oitpText += otemp
self.printDebug("GMX proper dihedrals done")
else:
self.printMess("Writing GMX dihedrals for GMX 4.5 and higher.\n")
funct = 9 # 9
for dih in self.properDihedralsGmx45:
a1 = dih[0][0].atomName
a2 = dih[0][1].atomName
a3 = dih[0][2].atomName
a4 = dih[0][3].atomName
id1 = dih[0][0].id
id2 = dih[0][1].id
id3 = dih[0][2].id
id4 = dih[0][3].id
ph = dih[1] # phase already in degree
kd = dih[2] * cal # kPhi PK
pn = dih[3] # .period
line = "%6i %6i %6i %6i %6i %8.2f %9.5f %3i ; %6s-%6s-%6s-%6s\n" % \
(id1, id2, id3, id4, funct, ph, kd, pn, a1, a2, a3, a4)
oline = "%6i %6i %6i %6i %6i ; %8.2f %9.5f %3i ; %6s-%6s-%6s-%6s\n" % \
(id1, id2, id3, id4, funct, ph, kd, pn, a1, a2, a3, a4)
temp.append(line)
otemp.append(oline)
temp.sort()
otemp.sort()
if temp:
if amb2gmx:
topText.append(headProDihGmx45)
topText += temp
else:
itpText.append(headProDihGmx45)
itpText += temp
oitpText.append(headProDihGmx45)
oitpText += otemp
# for properDihedralsAlphaGamma
if not self.gmx4:
funct = 4 # 4
else:
funct = 1
temp = []
otemp = []
for dih in self.properDihedralsAlphaGamma:
a1 = dih[0][0].atomName
a2 = dih[0][1].atomName
a3 = dih[0][2].atomName
a4 = dih[0][3].atomName
id1 = dih[0][0].id
id2 = dih[0][1].id
id3 = dih[0][2].id
id4 = dih[0][3].id
ph = dih[1] # phase already in degree
kd = dih[2] * cal # kPhi PK
pn = dih[3] # .period
line = "%6i %6i %6i %6i %6i %8.2f %9.5f %3i ; %6s-%6s-%6s-%6s\n" % \
(id1, id2, id3, id4, funct, ph, kd, pn, a1, a2, a3, a4)
oline = "%6i %6i %6i %6i %6i ; %8.2f %9.5f %3i ; %6s-%6s-%6s-%6s\n" % \
(id1, id2, id3, id4, funct, ph, kd, pn, a1, a2, a3, a4)
temp.append(line)
otemp.append(oline)
temp.sort()
otemp.sort()
if temp:
if amb2gmx:
topText.append(headProDihAlphaGamma)
topText += temp
else:
itpText.append(headProDihAlphaGamma)
itpText += temp
oitpText.append(headProDihAlphaGamma)
oitpText += otemp
self.printDebug("GMX special proper dihedrals done")
self.printDebug("improperDihedrals %i" % len(self.improperDihedrals))
temp = []
otemp = []
for dih in self.improperDihedrals:
a1 = dih.atoms[0].atomName
a2 = dih.atoms[1].atomName
a3 = dih.atoms[2].atomName
a4 = dih.atoms[3].atomName
id1 = dih.atoms[0].id
id2 = dih.atoms[1].id
id3 = dih.atoms[2].id
id4 = dih.atoms[3].id
kd = dih.kPhi * cal
pn = dih.period
ph = dih.phase * radPi
line = "%6i %6i %6i %6i %6i %8.2f %9.5f %3i ; %6s-%6s-%6s-%6s\n" % \
(id1, id2, id3, id4, funct, ph, kd, pn, a1, a2, a3, a4)
oline = "%6i %6i %6i %6i %6i ; %8.2f %9.5f %3i ; %6s-%6s-%6s-%6s\n" % \
(id1, id2, id3, id4, funct, ph, kd, pn, a1, a2, a3, a4)
temp.append(line)
otemp.append(oline)
temp.sort()
otemp.sort()
if temp:
if amb2gmx:
topText.append(headImpDih)
topText += temp
else:
itpText.append(headImpDih)
itpText += temp
oitpText.append(headImpDih)
oitpText += otemp
self.printDebug("GMX improper dihedrals done")
if not self.direct:
for ion in ionsSorted:
topText.append(ionsDict[ion[2]])
if nWat:
topText.append(headWater)
topText.append(headSystem % (self.baseName))
topText.append(headMols)
otopText.append(headSystem % (self.baseName))
otopText.append(headMols)
if nSolute > 0:
topText.append(" %-16s %-6i\n" % (self.baseName, nSolute))
otopText.append(" %-16s %-6i\n" % (self.baseName, nSolute))
if not self.direct:
for ion in ionsSorted:
topText.append(" %-16s %-6i\n" % (ion[2].upper(), ion[1]))
if nWat:
topText.append(" %-16s %-6i\n" % ('WAT', nWat))
gmxDir = os.path.abspath('.')
topFileName = os.path.join(gmxDir, top)
topFile = open(topFileName, 'w')
topFile.writelines(topText)
if not amb2gmx:
itpFileName = os.path.join(gmxDir, itp)
itpFile = open(itpFileName, 'w')
itpFile.writelines(itpText)
oitpFileName = os.path.join(gmxDir, oitp)
oitpFile = open(oitpFileName, 'w')
oitpFile.writelines(oitpText)
otopFileName = os.path.join(gmxDir, otop)
otopFile = open(otopFileName, 'w')
otopFile.writelines(otopText)
def writeGroFile(self):
# print "Writing GROMACS GRO file\n"
self.printDebug("writing GRO file")
gro = self.baseName + '_GMX.gro'
gmxDir = os.path.abspath('.')
groFileName = os.path.join(gmxDir, gro)
groFile = open(groFileName, 'w')
groFile.write(head % (gro, date))
groFile.write(" %i\n" % len(self.atoms))
count = 1
for atom in self.atoms:
coords = [c * 0.1 for c in atom.coords]
resid = atom.resid
line = "%5d%5s%5s%5d%8.3f%8.3f%8.3f\n" % \
(resid + 1, self.residueLabel[resid], atom.atomName,
count, coords[0], coords[1], coords[2])
count += 1
if count == 100000:
count = 0
groFile.write(line)
if self.pbc:
boxX = self.pbc[0][0] * 0.1
boxY = self.pbc[0][1] * 0.1
boxZ = self.pbc[0][2] * 0.1
vX = self.pbc[1][0]
# vY = self.pbc[1][1]
# vZ = self.pbc[1][2]
if vX == 90.0:
self.printDebug("PBC triclinic")
text = "%11.5f %11.5f %11.5f\n" % (boxX, boxY, boxZ)
elif round(vX, 2) == 109.47:
self.printDebug("PBC octahedron")
f1 = 0.471405 # 1/3 * sqrt(2)
f2 = 0.333333 * boxX
v22 = boxY * 2 * f1
v33 = boxZ * f1 * 1.73205 # f1 * sqrt(3)
v21 = v31 = v32 = 0.0
v12 = f2
v13 = -f2
v23 = f1 * boxX
text = "%11.5f %11.5f %11.5f %11.5f %11.5f %11.5f %11.5f %11.5f %11.5f\n" % \
(boxX, v22, v33, v21, v31, v12, v32, v13, v23)
else:
self.printDebug("Box size estimated")
X = [a.coords[0] * 0.1 for a in self.atoms]
Y = [a.coords[1] * 0.1 for a in self.atoms]
Z = [a.coords[2] * 0.1 for a in self.atoms]
boxX = max(X) - min(X) # + 2.0 # 2.0 is double of rlist
boxY = max(Y) - min(Y) # + 2.0
boxZ = max(Z) - min(Z) # + 2.0
text = "%11.5f %11.5f %11.5f\n" % (boxX * 20.0, boxY * 20.0, boxZ * 20.0)
groFile.write(text)
def writeMdpFiles(self):
emMdp = """; to test
; gmx grompp -f em.mdp -c {base}_GMX.gro -p {base}_GMX.top -o em.tpr -v
; gmx mdrun -ntmpi 1 -v -deffnm em
integrator = steep
nsteps = 500
""".format(base=self.baseName)
mdMdp = """; to test
; gmx grompp -f md.mdp -c em.gro -p {base}_GMX.top -o md.tpr
; gmx mdrun -ntmpi 1 -v -deffnm md
integrator = md
nsteps = 10000
""".format(base=self.baseName)
emMdpFile = open('em.mdp', 'w')
mdMdpFile = open('md.mdp', 'w')
emMdpFile.write(emMdp)
mdMdpFile.write(mdMdp)
def writeCnsTopolFiles(self):
autoAngleFlag = True
autoDihFlag = True
cnsDir = os.path.abspath('.')
pdb = self.baseName + '_NEW.pdb'
par = self.baseName + '_CNS.par'
top = self.baseName + '_CNS.top'
inp = self.baseName + '_CNS.inp'
pdbFileName = os.path.join(cnsDir, pdb)
parFileName = os.path.join(cnsDir, par)
topFileName = os.path.join(cnsDir, top)
inpFileName = os.path.join(cnsDir, inp)
self.CnsTopFileName = topFileName
self.CnsInpFileName = inpFileName
self.CnsParFileName = parFileName
self.CnsPdbFileName = pdbFileName
parFile = open(parFileName, 'w')
topFile = open(topFileName, 'w')
inpFile = open(inpFileName, 'w')
self.printMess("Writing NEW PDB file\n")
self.writePdb(pdbFileName)
self.printMess("Writing CNS/XPLOR files\n")
# print "Writing CNS PAR file\n"
parFile.write("Remarks " + head % (par, date))
parFile.write("\nset echo=false end\n")
parFile.write("\n{ Bonds: atomType1 atomType2 kb r0 }\n")
lineSet = []
for bond in self.bonds:
a1Type = bond.atoms[0].atomType.atomTypeName + '_'
a2Type = bond.atoms[1].atomType.atomTypeName + '_'
kb = 1000.0
if not self.allhdg:
kb = bond.kBond
r0 = bond.rEq
line = "BOND %5s %5s %8.1f %8.4f\n" % (a1Type, a2Type, kb, r0)
lineRev = "BOND %5s %5s %8.1f %8.4f\n" % (a2Type, a1Type, kb, r0)
if line not in lineSet:
if lineRev not in lineSet:
lineSet.append(line)
for item in lineSet:
parFile.write(item)
parFile.write("\n{ Angles: aType1 aType2 aType3 kt t0 }\n")
lineSet = []
for angle in self.angles:
a1 = angle.atoms[0].atomType.atomTypeName + '_'
a2 = angle.atoms[1].atomType.atomTypeName + '_'
a3 = angle.atoms[2].atomType.atomTypeName + '_'
kt = 500.0
if not self.allhdg:
kt = angle.kTheta
t0 = angle.thetaEq * radPi
line = "ANGLe %5s %5s %5s %8.1f %8.2f\n" % (a1, a2, a3, kt, t0)
lineRev = "ANGLe %5s %5s %5s %8.1f %8.2f\n" % (a3, a2, a1, kt, t0)
if line not in lineSet:
if lineRev not in lineSet:
lineSet.append(line)
for item in lineSet:
parFile.write(item)
parFile.write("\n{ Proper Dihedrals: aType1 aType2 aType3 aType4 kt per\
iod phase }\n")
lineSet = set()
for item in self.condensedProperDihedrals:
seq = ''
id_ = 0
for dih in item:
# id_ = item.index(dih)
l = len(item)
a1 = dih.atoms[0].atomType.atomTypeName + '_'
a2 = dih.atoms[1].atomType.atomTypeName + '_'
a3 = dih.atoms[2].atomType.atomTypeName + '_'
a4 = dih.atoms[3].atomType.atomTypeName + '_'
kp = 750.0
if not self.allhdg:
kp = dih.kPhi
p = dih.period
ph = dih.phase * radPi
if l > 1:
if id_ == 0:
line = "DIHEdral %5s %5s %5s %5s MULT %1i %7.3f %4i %8\
.2f\n" % (a1, a2, a3, a4, l, kp, p, ph)
else:
line = "%s %7.3f %4i %8.2f\n" % (40 * " ", kp, p, ph)
else:
line = "DIHEdral %5s %5s %5s %5s %15.3f %4i %8.2f\n" % (a1,
a2, a3, a4, kp, p, ph)
seq += line
id_ += 1
lineSet.add(seq)
for item in lineSet:
parFile.write(item)
parFile.write("\n{ Improper Dihedrals: aType1 aType2 aType3 aType4 kt p\
eriod phase }\n")
lineSet = set()
for idh in self.improperDihedrals:
a1 = idh.atoms[0].atomType.atomTypeName + '_'
a2 = idh.atoms[1].atomType.atomTypeName + '_'
a3 = idh.atoms[2].atomType.atomTypeName + '_'
a4 = idh.atoms[3].atomType.atomTypeName + '_'
kp = 750.0
if not self.allhdg:
kp = idh.kPhi
p = idh.period
ph = idh.phase * radPi
line = "IMPRoper %5s %5s %5s %5s %13.1f %4i %8.2f\n" % (a1, a2, a3,
a4, kp, p, ph)
lineSet.add(line)
if self.chiral:
for idhc in self.chiralGroups:
_atc, neig, angle = idhc
a1 = neig[0].atomType.atomTypeName + '_'
a2 = neig[1].atomType.atomTypeName + '_'
a3 = neig[2].atomType.atomTypeName + '_'
a4 = neig[3].atomType.atomTypeName + '_'
kp = 11000.0
p = 0
ph = angle
line = "IMPRoper %5s %5s %5s %5s %13.1f %4i %8.2f\n" % (a1, a2, a3,
a4, kp, p, ph)
lineSet.add(line)
for item in lineSet:
parFile.write(item)
parFile.write("\n{ Nonbonded: Type Emin sigma; (1-4): Emin/2 sigma }\n")
for at in self.atomTypes:
A = at.ACOEF
B = at.BCOEF
atName = at.atomTypeName + '_'
if B == 0.0:
sigma = epAmber = ep2 = sig2 = 0.0
else:
epAmber = 0.25 * B * B / A
ep2 = epAmber / 2.0
sigma = math.pow((A / B), (1.0 / 6))
sig2 = sigma
line = "NONBonded %5s %11.6f %11.6f %11.6f %11.6f\n" % (atName,
epAmber, sigma, ep2, sig2)
parFile.write(line)
parFile.write("\nset echo=true end\n")
# print "Writing CNS TOP file\n"
topFile.write("Remarks " + head % (top, date))
topFile.write("\nset echo=false end\n")
topFile.write("\nautogenerate angles=%s dihedrals=%s end\n" %
(autoAngleFlag, autoDihFlag))
topFile.write("\n{ atomType mass }\n")
for at in self.atomTypes:
atType = at.atomTypeName + '_'
mass = at.mass
line = "MASS %-5s %8.3f\n" % (atType, mass)
topFile.write(line)
topFile.write("\nRESIdue %s\n" % self.residueLabel[0])
topFile.write("\nGROUP\n")
topFile.write("\n{ atomName atomType Charge }\n")
for at in self.atoms:
atName = at.atomName
atType = at.atomType.atomTypeName + '_'
charge = at.charge
line = "ATOM %-5s TYPE= %-5s CHARGE= %8.4f END\n" % (atName, atType,
charge)
topFile.write(line)
topFile.write("\n{ Bonds: atomName1 atomName2 }\n")
for bond in self.bonds:
a1Name = bond.atoms[0].atomName
a2Name = bond.atoms[1].atomName
line = "BOND %-5s %-5s\n" % (a1Name, a2Name)
topFile.write(line)
if not autoAngleFlag or 1: # generating angles anyway
topFile.write("\n{ Angles: atomName1 atomName2 atomName3}\n")
for angle in self.angles:
a1Name = angle.atoms[0].atomName
a2Name = angle.atoms[1].atomName
a3Name = angle.atoms[2].atomName
line = "ANGLe %-5s %-5s %-5s\n" % (a1Name, a2Name, a3Name)
topFile.write(line)
if not autoDihFlag or 1: # generating angles anyway
topFile.write("\n{ Proper Dihedrals: name1 name2 name3 name4 }\n")
for item in self.condensedProperDihedrals:
for dih in item:
l = len(item)
a1Name = dih.atoms[0].atomName
a2Name = dih.atoms[1].atomName
a3Name = dih.atoms[2].atomName
a4Name = dih.atoms[3].atomName
line = "DIHEdral %-5s %-5s %-5s %-5s\n" % (a1Name, a2Name,
a3Name, a4Name)
break
topFile.write(line)
topFile.write("\n{ Improper Dihedrals: aName1 aName2 aName3 aName4 }\n")
for dih in self.improperDihedrals:
a1Name = dih.atoms[0].atomName
a2Name = dih.atoms[1].atomName
a3Name = dih.atoms[2].atomName
a4Name = dih.atoms[3].atomName
line = "IMPRoper %-5s %-5s %-5s %-5s\n" % (a1Name, a2Name, a3Name,
a4Name)
topFile.write(line)
if self.chiral:
for idhc in self.chiralGroups:
_atc, neig, angle = idhc
a1Name = neig[0].atomName
a2Name = neig[1].atomName
a3Name = neig[2].atomName
a4Name = neig[3].atomName
line = "IMPRoper %-5s %-5s %-5s %-5s\n" % (a1Name, a2Name, a3Name,
a4Name)
topFile.write(line)
topFile.write("\nEND {RESIdue %s}\n" % self.residueLabel[0])
topFile.write("\nset echo=true end\n")
# print "Writing CNS INP file\n"
inpFile.write("Remarks " + head % (inp, date))
inpData = \
"""
topology
@%(CNS_top)s
end
parameters
@%(CNS_par)s
nbonds
atom cdie shift eps=1.0 e14fac=0.4 tolerance=0.5
cutnb=9.0 ctonnb=7.5 ctofnb=8.0
nbxmod=5 vswitch wmin 1.0
end
remark dielectric constant eps set to 1.0
end
flags exclude elec ? end
segment name=" "
chain
coordinates @%(NEW_pdb)s
end
end
coordinates @%(NEW_pdb)s
coord copy end
! Remarks If you want to shake up the coordinates a bit ...
vector do (x=x+6*(rand()-0.5)) (all)
vector do (y=y+6*(rand()-0.5)) (all)
vector do (z=z+6*(rand()-0.5)) (all)
write coordinates output=%(CNS_ran)s end
! Remarks RMS diff after randomisation and before minimisation
coord rms sele=(known and not hydrogen) end
print threshold=0.02 bonds
print threshold=3.0 angles
print threshold=3.0 dihedrals
print threshold=3.0 impropers
! Remarks Do Powell energy minimisation
minimise powell
nstep=250 drop=40.0
end
write coordinates output=%(CNS_min)s end
write structure output=%(CNS_psf)s end
! constraints interaction (not hydro) (not hydro) end
print threshold=0.02 bonds
print threshold=3.0 angles
print threshold=3.0 dihedrals
print threshold=3.0 impropers
flags exclude * include vdw end energy end
distance from=(not hydro) to=(not hydro) cutoff=2.6 end
! Remarks RMS fit after minimisation
coord fit sele=(known and not hydrogen) end
stop
"""
dictInp = {}
dictInp['CNS_top'] = top
dictInp['CNS_par'] = par
dictInp['NEW_pdb'] = pdb
dictInp['CNS_min'] = self.baseName + '_NEW_min.pdb'
dictInp['CNS_psf'] = self.baseName + '_CNS.psf'
dictInp['CNS_ran'] = self.baseName + '_rand.pdb'
line = inpData % dictInp
inpFile.write(line)
if os.path.exists(self.obchiralExe):
self.printDebug("chiralGroups %i" % len(self.chiralGroups))
else:
self.printDebug("No 'obchiral' to process chiral atoms. Consider installing http://openbabel.org")
class ACTopol(AbstractTopol):
"""
Class to build the AC topologies (Antechamber AmberTools)
"""
def __init__(self, inputFile, chargeType='bcc', chargeVal=None,
multiplicity='1', atomType='gaff', force=False, basename=None,
debug=False, outTopol='all', engine='tleap', allhdg=False,
timeTol=36000, qprog='sqm', ekFlag=None, verbose=True,
gmx4=False, disam=False, direct=False, is_sorted=False, chiral=False):
self.debug = debug
self.verbose = verbose
self.gmx4 = gmx4
self.disam = disam
self.direct = direct
self.sorted = is_sorted
self.chiral = chiral
self.inputFile = os.path.basename(inputFile)
self.rootDir = os.path.abspath('.')
self.absInputFile = os.path.abspath(inputFile)
if not os.path.exists(self.absInputFile):
self.printWarn("input file doesn't exist")
baseOriginal, ext = os.path.splitext(self.inputFile)
base = basename or baseOriginal
self.baseOriginal = baseOriginal
self.baseName = base # name of the input file without ext.
self.timeTol = timeTol
self.printDebug("Max execution time tolerance is %s" % elapsedTime(self.timeTol))
self.ext = ext
if ekFlag == '"None"' or ekFlag is None:
self.ekFlag = ''
else:
self.ekFlag = '-ek %s' % ekFlag
self.extOld = ext
self.homeDir = self.baseName + '.acpype'
self.chargeType = chargeType
self.chargeVal = chargeVal
self.multiplicity = multiplicity
self.atomType = atomType
self.gaffDatfile = 'gaff.dat'
leapGaffFile = 'leaprc.gaff'
if '2' in self.atomType:
leapGaffFile = 'leaprc.gaff2'
self.gaffDatfile = 'gaff2.dat'
self.force = force
self.engine = engine
self.allhdg = allhdg
self.acExe = ''
dirAmber = os.getenv('AMBERHOME', os.getenv('ACHOME'))
if dirAmber:
for ac_bin in ['bin', 'exe']:
ac_path = os.path.join(dirAmber, ac_bin, 'antechamber')
if os.path.exists(ac_path):
self.acExe = ac_path
break
if not self.acExe:
self.acExe = _getoutput('which antechamber') or '' # '/Users/alan/Programmes/antechamber-1.27/exe/antechamber'
if not os.path.exists(self.acExe):
self.printError("no 'antechamber' executable!")
return None
self.tleapExe = _getoutput('which tleap') or ''
self.sleapExe = _getoutput('which sleap') or ''
self.parmchkExe = _getoutput('which parmchk2') or ''
self.babelExe = _getoutput('which babel') or ''
if not os.path.exists(self.babelExe):
if self.ext != '.mol2' and self.ext != '.mdl': # and self.ext != '.mol':
self.printError("no 'babel' executable; you need it if input is PDB")
self.printError("otherwise use only MOL2 or MDL file as input ... aborting!")
sys.exit(1)
else:
self.printWarn("no 'babel' executable, no PDB file as input can be used!")
acBase = base + '_AC'
self.acBaseName = acBase
self.acXyzFileName = acBase + '.inpcrd'
self.acTopFileName = acBase + '.prmtop'
self.acFrcmodFileName = acBase + '.frcmod'
self.tmpDir = os.path.join(self.rootDir, '.acpype_tmp_%s' % os.path.basename(base))
self.setResNameCheckCoords()
self.guessCharge()
acMol2FileName = '%s_%s_%s.mol2' % (base, chargeType, atomType)
self.acMol2FileName = acMol2FileName
self.charmmBase = '%s_CHARMM' % base
# check for which version of antechamber
if 'amber10' in self.acExe:
if qprog == 'sqm':
self.printWarn("SQM is not implemented in AmberTools 1.2")
self.printWarn("Setting mopac for antechamber")
qprog = 'mopac'
elif qprog == 'divcon':
if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)):
self.printWarn("DIVCON is not installed")
self.printWarn("Setting mopac for antechamber")
qprog = 'mopac'
elif 'amber1' in self.acExe:
if qprog == 'divcon':
self.printWarn("DIVCON is not implemented in AmberTools > 1.3 anymore")
self.printWarn("Setting sqm for antechamber")
qprog = 'sqm'
elif qprog == 'mopac':
if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)):
self.printWarn("MOPAC is not installed")
self.printWarn("Setting sqm for antechamber")
return None
qprog = 'sqm'
else:
self.printWarn("Old version of antechamber. Strongly consider upgrading to AmberTools")
self.printWarn("Setting mopac for antechamber")
qprog = 'mopac'
self.qFlag = qDict[qprog]
self.outTopols = [outTopol]
if outTopol == 'all':
self.outTopols = outTopols
self.acParDict = {'base': base, 'ext': ext[1:], 'acBase': acBase,
'acMol2FileName': acMol2FileName, 'res': self.resName,
'leapAmberFile': leapAmberFile, 'baseOrg': self.baseOriginal,
'leapGaffFile': leapGaffFile}
class MolTopol(ACTopol):
""""
Class to write topologies and parameters files for several applications
http://amber.scripps.edu/formats.html (not updated to amber 10 yet)
Parser, take information in AC xyz and top files and convert to objects
INPUTS: acFileXyz and acFileTop
RETURN: molTopol obj or None
"""
def __init__(self, acTopolObj=None, acFileXyz=None, acFileTop=None,
debug=False, basename=None, verbose=True, gmx4=False,
disam=False, direct=False, is_sorted=False, chiral=False):
self.chiral = chiral
self.obchiralExe = _getoutput('which obchiral') or ''
self.allhdg = False
self.debug = debug
self.gmx4 = gmx4
self.disam = disam
self.direct = direct
self.sorted = is_sorted
self.verbose = verbose
self.inputFile = acFileTop
if acTopolObj:
if not acFileXyz:
acFileXyz = acTopolObj.acXyzFileName
if not acFileTop:
acFileTop = acTopolObj.acTopFileName
self._parent = acTopolObj
self.allhdg = self._parent.allhdg
self.debug = self._parent.debug
self.inputFile = self._parent.inputFile
if not os.path.exists(acFileXyz) and not os.path.exists(acFileTop):
self.printError("Files '%s' and '%s' don't exist")
self.printError("molTopol object won't be created")
return None
# if not os.path.exists(self.obchiralExe) and self.chiral:
# self.printError("no 'obchiral' executable, it won't work to store non-planar improper dihedrals!")
# self.printWarn("Consider installing http://openbabel.org")
self.xyzFileData = open(acFileXyz, 'r').readlines()
self.topFileData = open(acFileTop, 'r').readlines()
self.printDebug("prmtop and inpcrd files loaded")
# self.pointers = self.getFlagData('POINTERS')
self.getResidueLabel()
if len(self.residueLabel) > 1:
self.baseName = basename or os.path.splitext(os.path.basename(acFileTop))[0] # 'solute'
else:
self.baseName = basename or self.residueLabel[0] # 3 caps letters
if acTopolObj:
self.baseName = basename or acTopolObj.baseName
self.printDebug("basename defined = '%s'" % self.baseName)
self.getAtoms()
self.getBonds()
self.getAngles()
self.getDihedrals()
self.getChirals()
if not os.path.exists(self.obchiralExe) and self.chiral:
self.printError("no 'obchiral' executable, it won't work to store non-planar improper dihedrals!")
self.printWarn("Consider installing http://openbabel.org")
elif self.chiral and not self.chiralGroups:
self.printWarn("No chiral atoms found")
# self.setAtomPairs()
# self.getExcludedAtoms()
# a list of FLAGS from acTopFile that matter
# self.flags = ( 'POINTERS', 'ATOM_NAME', 'CHARGE', 'MASS', 'ATOM_TYPE_INDEX',
# 'NUMBER_EXCLUDED_ATOMS', 'NONBONDED_PARM_INDEX',
# 'RESIDUE_LABEL', 'BOND_FORCE_CONSTANT', 'BOND_EQUIL_VALUE',
# 'ANGLE_FORCE_CONSTANT', 'ANGLE_EQUIL_VALUE',
# 'DIHEDRAL_FORCE_CONSTANT', 'DIHEDRAL_PERIODICITY',
# 'DIHEDRAL_PHASE', 'AMBER_ATOM_TYPE' )
# Sort atoms for gromacs output. # JDC
if self.sorted:
self.printMess("Sorting atoms for gromacs ordering.\n")
self.sortAtomsForGromacs()
class Atom(object):
"""
Charges in prmtop file has to be divide by 18.2223 to convert to charge
in units of the electron charge.
To convert ACOEF and BCOEF to r0 (Ang.) and epsilon (kcal/mol), as seen
in gaff.dat for example; same atom type (i = j):
r0 = 1/2 * (2 * ACOEF/BCOEF)^(1/6)
epsilon = 1/(4 * A) * BCOEF^2
To convert r0 and epsilon to ACOEF and BCOEF
ACOEF = sqrt(ep_i * ep_j) * (r0_i + r0_j)^12
BCOEF = 2 * sqrt(ep_i * ep_j) * (r0_i + r0_j)^6
= 2 * ACOEF/(r0_i + r0_j)^6
where index i and j for atom types.
Coord is given in Ang. and mass in Atomic Mass Unit.
"""
def __init__(self, atomName, atomType, id_, resid, mass, charge, coord):
self.atomName = atomName
self.atomType = atomType
self.id = id_
self.cgnr = id_
self.resid = resid
self.mass = mass
self.charge = charge # / qConv
self.coords = coord
def __str__(self):
return '<Atom id=%s, name=%s, %s>' % (self.id, self.atomName, self.atomType)
def __repr__(self):
return '<Atom id=%s, name=%s, %s>' % (self.id, self.atomName, self.atomType)
class AtomType(object):
"""
AtomType per atom in gaff or amber.
"""
def __init__(self, atomTypeName, mass, ACOEF, BCOEF):
self.atomTypeName = atomTypeName
self.mass = mass
self.ACOEF = ACOEF
self.BCOEF = BCOEF
def __str__(self):
return '<AtomType=%s>' % self.atomTypeName
def __repr__(self):
return '<AtomType=%s>' % self.atomTypeName
class Bond(object):
"""
attributes: pair of Atoms, spring constant (kcal/mol), dist. eq. (Ang)
"""
def __init__(self, atoms, kBond, rEq):
self.atoms = atoms
self.kBond = kBond
self.rEq = rEq
def __str__(self):
return '<%s, r=%s>' % (self.atoms, self.rEq)
def __repr__(self):
return '<%s, r=%s>' % (self.atoms, self.rEq)
class Angle(object):
"""
attributes: 3 Atoms, spring constant (kcal/mol/rad^2), angle eq. (rad)
"""
def __init__(self, atoms, kTheta, thetaEq):
self.atoms = atoms
self.kTheta = kTheta
self.thetaEq = thetaEq # rad, to convert to degree: thetaEq * 180/Pi
def __str__(self):
return '<%s, ang=%.2f>' % (self.atoms, self.thetaEq * 180 / Pi)
def __repr__(self):
return '<%s, ang=%.2f>' % (self.atoms, self.thetaEq * 180 / Pi)
class Dihedral(object):
"""
attributes: 4 Atoms, spring constant (kcal/mol), periodicity,
phase (rad)
"""
def __init__(self, atoms, kPhi, period, phase):
self.atoms = atoms
self.kPhi = kPhi
self.period = period
self.phase = phase # rad, to convert to degree: kPhi * 180/Pi
def __str__(self):
return '<%s, ang=%.2f>' % (self.atoms, self.phase * 180 / Pi)
def __repr__(self):
return '<%s, ang=%.2f>' % (self.atoms, self.phase * 180 / Pi)
if __name__ == '__main__':
t0 = time.time()
print(header)
parser = optparse.OptionParser(usage=usage + epilog)
parser.add_option('-i', '--input',
action="store",
dest='input',
help="input file name with either extension '.pdb', '.mdl' or '.mol2' (mandatory if -p and -x not set)",)
parser.add_option('-b', '--basename',
action="store",
dest='basename',
help='a basename for the project (folder and output files)',)
parser.add_option('-x', '--inpcrd',
action="store",
dest='inpcrd',
help="amber inpcrd file name (always used with -p)",)
parser.add_option('-p', '--prmtop',
action="store",
dest='prmtop',
help="amber prmtop file name (always used with -x)",)
parser.add_option('-c', '--charge_method',
type='choice',
choices=['gas', 'bcc', 'user'],
action="store",
default='bcc',
dest='charge_method',
help="charge method: gas, bcc (default), user (user's charges in mol2 file)",)
parser.add_option('-n', '--net_charge',
action="store",
type='int',
default=0,
dest='net_charge',
help="net molecular charge (int), for gas default is 0",)
parser.add_option('-m', '--multiplicity',
action="store",
type='int',
default=1,
dest='multiplicity',
help="multiplicity (2S+1), default is 1",)
parser.add_option('-a', '--atom_type',
type='choice',
choices=['gaff', 'amber', 'gaff2', 'amber2'], # , 'bcc', 'sybyl']
action="store",
default='gaff',
dest='atom_type',
help="atom type, can be gaff, gaff2, amber (AMBER14SB) or amber2 (AMBER14SB + GAFF2), default is gaff",)
parser.add_option('-q', '--qprog',
type='choice',
choices=['mopac', 'sqm', 'divcon'],
action="store",
default='sqm',
dest='qprog',
help="am1-bcc flag, sqm (default), divcon, mopac",)
parser.add_option('-k', '--keyword',
action="store",
dest='keyword',
help="mopac or sqm keyword, inside quotes",)
parser.add_option('-f', '--force',
action="store_true",
dest='force',
help='force topologies recalculation anew',)
parser.add_option('-d', '--debug',
action="store_true",
dest='debug',
help='for debugging purposes, keep any temporary file created',)
parser.add_option('-o', '--outtop',
type='choice',
choices=['all'] + outTopols,
action="store",
default='all',
dest='outtop',
help="output topologies: all (default), gmx, cns or charmm",)
parser.add_option('-z', '--gmx4',
action="store_true",
dest='gmx4',
help='write RB dihedrals old GMX 4.0',)
parser.add_option('-t', '--cnstop',
action="store_true",
dest='cnstop',
help='write CNS topology with allhdg-like parameters (experimental)',)
parser.add_option('-e', '--engine',
type='choice',
choices=['tleap', 'sleap'],
action="store",
default='tleap',
dest='engine',
help="engine: tleap (default) or sleap (not fully matured)",)
parser.add_option('-s', '--max_time',
action="store",
type='int',
default=36000,
dest='max_time',
help="max time (in sec) tolerance for sqm/mopac, default is 10 hours",)
parser.add_option('-y', '--ipython',
action="store_true",
dest='ipython',
help='start iPython interpreter',)
parser.add_option('-w', '--verboseless',
action="store_false",
default=True,
dest='verboseless',
help='print nothing',)
parser.add_option('-g', '--disambiguate',
action="store_true",
dest='disambiguate',
help='disambiguate lower and uppercase atomtypes in GMX top file',)
parser.add_option('-u', '--direct',
action="store_true",
dest='direct',
help="for 'amb2gmx' mode, does a direct conversion, for any solvent",)
parser.add_option('-l', '--sorted',
action="store_true",
dest='sorted',
help="sort atoms for GMX ordering",)
parser.add_option('-j', '--chiral',
action="store_true",
dest='chiral',
help="create improper dihedral parameters for chiral atoms in CNS",)
options, remainder = parser.parse_args()
amb2gmx = False
# if options.chiral:
# options.cnstop = True
if not options.input:
amb2gmx = True
if not options.inpcrd or not options.prmtop:
parser.error("missing input files")
elif options.inpcrd or options.prmtop:
parser.error("either '-i' or ('-p', '-x'), but not both")
if options.debug:
text = "Python Version %s" % verNum
print('DEBUG: %s' % text)
if options.direct and not amb2gmx:
parser.error("option -u is only meaningful in 'amb2gmx' mode")
try:
if amb2gmx:
print("Converting Amber input files to Gromacs ...")
system = MolTopol(acFileXyz=options.inpcrd, acFileTop=options.prmtop,
debug=options.debug, basename=options.basename,
verbose=options.verboseless, gmx4=options.gmx4,
disam=options.disambiguate, direct=options.direct,
is_sorted=options.sorted, chiral=options.chiral)
system.printDebug("prmtop and inpcrd files parsed")
system.writeGromacsTopolFiles(amb2gmx=True)
else:
molecule = ACTopol(options.input, chargeType=options.charge_method,
chargeVal=options.net_charge, debug=options.debug,
multiplicity=options.multiplicity, atomType=options.atom_type,
force=options.force, outTopol=options.outtop,
engine=options.engine, allhdg=options.cnstop,
basename=options.basename, timeTol=options.max_time,
qprog=options.qprog, ekFlag='''"%s"''' % options.keyword,
verbose=options.verboseless, gmx4=options.gmx4,
disam=options.disambiguate, direct=options.direct,
is_sorted=options.sorted, chiral=options.chiral)
if not molecule.acExe:
molecule.printError("no 'antechamber' executable... aborting ! ")
hint1 = "HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?"
hint2 = "HINT2: is 'antechamber' in your $PATH?\n What 'which antechamber' in your terminal says?\n 'alias' doesn't work for ACPYPE."
molecule.printMess(hint1)
molecule.printMess(hint2)
sys.exit(1)
molecule.createACTopol()
molecule.createMolTopol()
acpypeFailed = False
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
print("ACPYPE FAILED: %s" % exceptionValue)
if options.debug:
traceback.print_tb(exceptionTraceback, file=sys.stdout)
acpypeFailed = True
execTime = int(round(time.time() - t0))
if execTime == 0:
msg = "less than a second"
else:
msg = elapsedTime(execTime)
print("Total time of execution: %s" % msg)
if options.ipython:
try:
from IPython.Shell import IPShellEmbed # @UnresolvedImport @UnusedImport
except:
from IPython.frontend.terminal.embed import InteractiveShellEmbed as IPShellEmbed # @UnresolvedImport @Reimport
ipshell = IPShellEmbed()
ipshell()
try:
rmtree(molecule.tmpDir)
except:
pass
if acpypeFailed:
sys.exit(1)
try:
os.chdir(molecule.rootDir)
except:
pass