View LIN_FIX.py
# THIS PROGRAM IS CREATED TO FIX PROBLEM WITH LINEAR MOLECULES
# WORKS ONLY FOR MOLECULES WITH ONE LINEAR BOND
import pandas as pd
import numpy as np
import os
import sys
def Refine_Zmat(zmat):
for l in range(len(zmat)):
View OMM_GRACE.sh
#!/bin/bash
#SBATCH --partition=gpu
#SBATCH --job-name=install
#SBATCH --ntasks=1 --nodes=1
#SBATCH --mem-per-cpu=6000
View BioPythonModules.py
# Using BioPython Doing All the Manipulations
##
import numpy as np
from Bio.PDB import *
from Bio.KDTree import KDTree
import pandas as pd
import warnings
from Bio import BiopythonWarning
warnings.simplefilter('ignore', BiopythonWarning)
View Delete_Clashes.py
## Using BioPython Doing All the Manipulations
##
import numpy as np
from Bio.PDB import *
from Bio.KDTree import KDTree
parser_p = PDBParser()
parser_m = PDBParser()
#3eiy_stripped.pdb LSD_POPE.pdb
View groITP2namdTOP.py
import pandas as pd
import numpy as np
import sys
def Get_topology(name_itp):
itp = open(name_itp, 'r')
itp_lines = []
for line in itp:
line.strip()
line = line.split(';')[0]
if line:itp_lines.append(line.strip())
View BNZ.rtf
! LigParGen generated RFT file for NAMD/CHARMM
MASS 1 C800 12.0110 C
MASS 2 C801 12.0110 C
MASS 3 C802 12.0110 C
MASS 4 H803 1.0080 H
MASS 5 C804 12.0110 C
MASS 6 H805 1.0080 H
MASS 7 C806 12.0110 C
MASS 8 H807 1.0080 H
MASS 9 C808 12.0110 C
View BNZ.prm
! LigParGen generated PRM file for NAMD/CHARMM
BOND
C801 C800 469.000 1.400
C802 C800 469.000 1.400
H803 C800 367.000 1.080
C804 C801 469.000 1.400
H805 C801 367.000 1.080
C806 C804 469.000 1.400
H807 C804 367.000 1.080
View combine_ITP.py
def read_itp(itp_name):
lines = open(itp_name).readlines()
impDat = []
for n in range(len(lines)):
if '[' in lines[n]: impDat.append(n)
atom_def = lines[impDat[0]+1:impDat[1]]
rest_mol = lines[impDat[1]:]
return(atom_def,rest_mol)
a_UNK,r_UNK=read_itp('UNK.itp')
a_OCT,r_OCT=read_itp('OCT.itp')
View center.sh
#!/usr/bin/env bash
TRAJIN=traj.xtc
TRAJOUT=trajfin.xtc
# delete the trajectory so gromacs wont display silly backup messages
if [ -e $TRAJOUT ]
then
rm -f $TRAJOUT
fi
View center.sh
#!/usr/bin/env bash
TRAJIN=traj.xtc
TRAJOUT=trajfin.xtc
# delete the trajectory so gromacs wont display silly backup messages
if [ -e $TRAJOUT ]
then
rm -f $TRAJOUT
fi