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#!/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 |
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#!/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 |
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#PBS -l nodes=2:ppn=12 | |
#PBS -N JobName | |
cd ${PBS_O_WORKDIR} | |
NPROCS=`wc -l <$PBS_NODEFILE` | |
MPIRUN="mpirun -machinefile $PBS_NODEFILE -n $NPROC" | |
export GMX_MAXBACKUP=1000 # max number of gro backup | |
GMDIR=/home/kmtu/local/gromacs-4.6.6/bin |
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import itertools | |
import mdtraj, mdtraj.geometry | |
import pandas as pd | |
traj = mdtraj.load("./traj.xtc", top="native.pdb") | |
top, bonds = traj.top.to_dataframe() | |
atoms = np.array(["H", "HA", "N", "CA", "C", "CB"]) |
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#!/usr/bin/env python | |
import sys | |
from prody import * | |
from rdkit import Chem | |
from rdkit.Chem import AllChem | |
from io import StringIO | |
import pypdb | |
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#!/usr/bin/env python | |
import sys | |
import os | |
from rdkit import Chem | |
def molecule_supplier_from_name(input_file_name): | |
ext = os.path.splitext(input_file_name)[-1] | |
if ext == ".smi": |
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#!/usr/bin/env python | |
# coding: utf-8 | |
########################################################################## | |
# this script was generated by openmm-builder. to customize it further, | |
# you can save the file to disk and edit it with your favorite editor. | |
########################################################################## | |
# REQUIRES: | |
# * OpenMM (core dynamics) |
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#!/usr/bin/env python | |
"""Sequence-based structural alignment of two proteins.""" | |
import argparse | |
import pathlib | |
from Bio.PDB import FastMMCIFParser, MMCIFIO, PDBParser, PDBIO, Superimposer | |
from Bio.PDB.Polypeptide import is_aa |