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GenerateFF.py
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GenerateFF.py
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# _*_ coding: utf-8 _*_
'''
@author: Ruan Yang
Created on 2018.5.7
Anaconda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/
Openbabel-2.4.1: http://openbabel.org/wiki/Main_Page
Antechamber: http://ambermd.org/antechamber/ac.html
Gaussian: http://gaussian.com/
Acpype.py: https://github.com/t-/acpype
amber2lammpsry.py: Can be find in lammps/tools/ directory. I modified the input/output file name.
PACKMOL: http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml
'''
import os
import numpy as np
# Ellement Mol mass
# Reference: https://ptable.com/
molmass={'H':1.008,
'HE':4.003,
'LI':6.941,
'BE':9.012,
'B':10.81,
'C':12.01,
'N':14.01,
'O':16.00,
'F':19.00,
'NE':20.18,
'NA':22.99,
'MG':24.31,
'AL':26.98,
'SI':28.09,
'P':30.97,
'S':32.06,
'CL':35.45,
'AR':39.95,
'K':39.10,
'CA':40.08,
'SC':44.96,
'TI':47.87,
'V':50.94,
'CR':52.00,
'MN':54.94,
'FE':55.85,
'CO':58.93,
'NI':58.69,
'CU':63.55,
'ZN':65.58,
'GA':69.72,
'GE':72.63,
'AS':74.92,
'SE':78.96,
'BR':79.90,
'KR':83.80,
'RB':85.47,
'SR':87.62,
'Y':88.91,
'ZR':91.22,
'NB':92.91,
'MO':95.96,
'TC':98.00,
'RU':101.1,
'RH':102.9,
'PD':106.4,
'AG':107.9,
'CD':112.4,
'IN':114.8,
'SN':118.7,
'SB':121.8,
'TE':127.6,
'I':126.9,
'XE':131.3,
'CS':133,
'BA':137.3,
'LA':139.0,
'CE':140.0,
'PR':141.0,
'ND':144.0,
'PM':145,
'SM':150.5,
'EU':152,
'GD':157,
'TB':159,
'DY':162.5,
'HO':165,
'ER':167,
'TM':169,
'YB':173,
'LU':175,
'HF':178.5,
'TA':181,
'W':184,
'RE':186,
'OS':190.0,
'IR':192,
'PT':195,
'AU':197,
'HG':200.6,
'TL':204.5,
'PB':207,
'BI':209,
'PO':209,
'AT':210,
'RN':222,
'FR':223,
'RA':226,
'AC':227,
'TH':232,
'PA':231,
'U':238,
'NP':237,
'PU':244,
'AM':243,
'CM':247,
'BK':247,
'CF':251,
'ES':252,
'FM':257,
'MD':258,
'NO':259,
'LR':260,
'RF':261,
'DB':262,
'SG':263,
'BH':264,
'HS':265,
'MT':266,
'DS':269,
'RG':272,
'CN':277,
'NH':286,
'FL':289,
'MC':289,
'LV':294,
'TS':294,
'OG':294}
# Output Element table to check
#for k,v in molmass.items():
# print("%s %.2f"%(k,v))
# Define load molecule smi format file function
# File format: #Compound ID SMILES
# Reference:Machine Learning of Partial Charges Derived From High-Quality
# Quantum-Mechanical Calculations.
# DOI: 10.1021/acs.jcim.7b00663
def loadData(filename):
'''
filename: input molecule smi
'''
name=[]
smi=[]
with open(filename,'r') as f:
lines=f.readlines()
for line in lines:
words=line.strip().split()
if words[1] == 'ID':
continue
else:
name.append(words[0])
smi.append(words[1])
return name,smi
# Use openbabel python library pybel convert smi to mol2
def Smi2mol2(molname,molsmi,molformat='mol2',platform='windows'):
'''
molname : molecule name
molsmi : molecule smiles format
molformat default value : 'mol2'
pltform : windows or linux, default windows
'''
if platform=='windows':
import pybel
mol=pybel.readstring("smi","%s"%(molsmi))
mol.make3D()
mol.write("%s"%(molformat),"%s%s%s"%(molname,'.',molformat))
if platform=='linux':
import openbabel
pass
# Through read mol2 file get the molecule mol mass
def readmol2(filename):
'''
filename : molecule_name.mol2
return value:
M: molecule mol mass
tcharge: total charge of molecules (charge value rstore in .mol2)
element: get the unique element in molecules
atoms: total atoms in one molecule
'''
M=0.0
tcharge=0.0
element=[]
with open(filename,'r') as f:
lines=f.readlines()
for line in lines:
words=line.split()
if(len(words)==5):
atoms=int(words[0])
bonds=int(words[1])
for line in lines[7:7+atoms:1]:
words=line.split()
for k,v in molmass.items():
if words[1]==k:
M += v
tcharge += float(words[-1])
element.append(words[1])
element=set(element)
return M,tcharge,element,atoms
# function nmolecule used to calculated the number of molecules
# packed into the box. The default size of the box 0. 0. 0. 40. 40. 40.
# Ameldeo Avogadro constant = 6.02×10^23/mol
# density=mass/volume
# mass = n*M
# number = (density*volume)/(M*Av)
def nmolecule(Molmass,box,freesol="off"):
'''
Molmass : single molecule molar mass
box : box size (xlo,ylo,zho,xhi,yhi,zhi)
return value: nmol the number of molecules in pack box, density = 1000 kg/m3
freesol: generated 1 organic + nmol water system. default='off'
'''
Molwater=16.00+1.008*2
Avc=6.02*(10**(23))
density=1000.0 #g/m3
volume=(box[3]-box[0])*(box[4]-box[1])*(box[5]-box[2])*(10**(-27)) # m3
if freesol=="on":
nmol=round(((density*volume*Avc)-Molmass)/Molwater)
else:
nmol=round((density*volume)/(Molmass*(1/Avc)))-1
return nmol
# First write PACKMOL input file, just pack single molecule
# into big box
def Packmolinputfile(inpname,filetype,number,box,freesol="off",method='GaussianAntechamber'):
'''
inpname : The name of the .inp file ,default = molecule name defined in .smi
filetype : .xyz or .pdb
number : number of molecules packed into simulation box
box : box size (xlo,ylo,zho,xhi,yhi,zhi)
freesol: True ,defaule=false
method : Generated molecule topology file method, default = GaussianAntechamber
'''
with open('%s.inp'%(inpname),'w') as f:
f.write('# This file generated by writeinputfile.py. Author: Ruan Yang\n')
f.write(' \n')
f.write('tolerance 2.0\n')
f.write('filetype %s\n'%(filetype))
f.write('output %s%s%s%s\n'%(inpname,'_pack','.',filetype))
f.write('add_box_sides 1.5\n')
f.write(' \n')
if(method=="acpypeantechamber"):
f.write('structure %s%s%s%s\n'%(inpname,'_NEW','.',filetype))
else:
f.write('structure %s%s%s\n'%(inpname,'.',filetype))
if freesol=="on":
f.write(' number %d\n'%(1))
f.write(' fixed %.2f %.2f %.2f 0. 0. 0.\n'%(box[3],box[4],box[5]))
f.write('end structure\n')
f.write('\n')
f.write('structure %s%s%s\n'%("water",'.',filetype))
f.write(' number %d\n'%(number))
f.write(' inside box %.2f %.2f %.2f %.2f %.2f %.2f\n'%(box[0],box[1],box[2],\
box[3],box[4],box[5]))
f.write('end structure\n')
else:
f.write(' number %d\n'%(number))
f.write(' inside box %.2f %.2f %.2f %.2f %.2f %.2f\n'%(box[0],box[1],box[2],\
box[3],box[4],box[5]))
f.write('end structure\n')
# Just used acpype.py generated gromacs,AMBER,CHARMM input file.
# for gromacs there have two force field: AMBER and OPLS/AA
# usage: python acpype.py -i mobley_5857.mol2 -b mobley_5857 -c user \
# -n 0 -o gmx -a gaff2 -d
# -i: default input molecule file format .mol2
# mobley_5857: molecule name
# -c: use charge define in .mol2
# -n: net charge 0
# -o: write gromacs topology file
# -a: atom type (default=gaff, I want use gaff2)
# -d: for debugging purposes, keep any temporary file created
def acpypeantechamber(molname,nmol,data='off'):
'''
molname : molecule name
nmol : number of molecules packed into simulation box
data : generated lammps data file, default='off'
'''
with open('acpypeantechamber.sh','w') as f:
f.write('#!/usr/bin/env python3 \n')
f.write(' \n')
f.write('python3 acpype.py -i %s.mol2 -b %s -c user -n 0 -o gmx \
-a gaff2 -d\n'%(molname,molname))
if data=='on':
f.write('python2 amber2lammpsry.py %s\n'%(molname))
f.write('packmol < *.inp\n')
print('sed -i " s/TST 1 /TST %d/g " TST_GMX.top\n'%(nmol),file=f)
# Define function write Gaussian and antechamber input file.
# Please reference: http://ambermd.org/tutorials/ForceField.php
# We fitting Energy landspace to get the RESP charges.
# We used .prmtop and inpcrd file, only output GAFF topology.
def GaussianAntechamber(molname,nmol,basisset='#HF/6-31G*',data='off',freesol="off"):
'''
molname : molecule name
nmol : number of molecules packed into simulation box
basisset : the basis set in Gaussian, default='#HF/6-31G*',(B3LYP/6-311G(d,p))
data : generated lammps data file, default='off'
'''
with open('GaussianAntechamber.sh','w') as f:
f.write('#!/bin/bash\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('# Reference: http://ambermd.org/tutorials/ForceField.php\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write(' \n')
# ''%%'' == %
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 1: prepare Gaussian input file .com"\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('antechamber -i %s.mol2 -fi mol2 -o %s.com -fo \
gcrt -pf y -gm "%%mem=4096MB" -gn "%%nproc=8" -nc 0 -gk \
"%s SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6)"\n'%(molname,molname,basisset))
f.write(' \n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 2: run Gaussian jobs."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('nohup g09 %s.com > %s.log &\n'%(molname,molname))
f.write('wait \n')
f.write(' \n')
#f.write('mv %s.log %s.out \n'%(molname,molname))
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 3: fitting Energy landspace get the RESP charge."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('antechamber -i %s.log -fi gout -o %s.mol2 -fo mol2 -c resp -rn TST \n'%(molname,molname))
f.write(' \n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 4: Get the atom deficiency force field parameters."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('parmchk2 -i %s.mol2 -f mol2 -o %s.frcmod \n'%(molname,molname))
f.write(' \n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 5: Using tleap get amber input file .inpcrd and .prmtop."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('tleap -f leap.in \n')
f.write(' \n')
# acpype.py used python2 interpreter
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 6: Using acpype.py get GROMACS topology and coordinate file."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('python2 ../../acpype.py -p %s.prmtop -x %s.inpcrd -c user -n 0 -d\n'%(molname,molname))
f.write(' \n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 7: Using packmol get the packed coordinate."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('packmol < *.inp\n')
f.write(' \n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 8: Adjust the .top file molecules number information."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
if freesol=="on":
print('sed -i "s/TST 1 /TST %d/g" TST_GMX.top\n'%(1),file=f)
f.write('echo SOL %d >> TST_GMX.top\n'%(nmol))
print('sed -i \'/defaults/i\#include "amber03.ff/forcefield.itp"\' TST_GMX.top',file=f)
#print('sed -i \'/moleculetype/i\#include "amber03.ff/tip3p.itp"\' TST_GMX.top',file=f)
print('sed -i \'/moleculetype/i\#include "amber03.ff/tip3p.itp"\\n\' TST_GMX.top',file=f)
print('sed -i \'/defaults/d\' TST_GMX.top',file=f)
print('sed -i \'/; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ/d\' TST_GMX.top',file=f)
print('sed -i \'/1 2 yes 0.5 0.8333/d\' TST_GMX.top',file=f)
else:
print('sed -i "s/TST 1 /TST %d/g" TST_GMX.top\n'%(nmol),file=f)
f.write(' \n')
if data=='on':
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('echo "Step 9: Generated lammps data file."\n')
f.write('echo "#-----------------------------------------------------------#"\n')
f.write('python2 ../../amber2lammpsry.py %s \n'%(molname[i]))
f.write(' \n')
with open('leap.in','w') as f:
f.write('source leaprc.ff14SB\n')
f.write('source leaprc.gaff\n')
f.write('loadamberparams %s.frcmod\n'%(molname))
f.write('%s=loadmol2 %s.mol2\n'%(molname,molname))
f.write('check %s\n'%(molname))
f.write('saveamberparm %s %s.prmtop %s.inpcrd\n'%(molname,molname,molname))
f.write('savepdb %s %s.pdb\n'%(molname,molname))
f.write('quit\n')