View NAMD_CPU_Grace.sh
#!/bin/bash
#BSUB -o . ## requests outfile be generated
#BSUB -a openmpi
#BSUB -q shared ## specify queue to run on, shared = default
#BSUB -J F_WIND ## job-name
#BSUB -W 24:00 ## walltime <HH:MM>= 24 hrs
#BSUB -n 4
module load Apps/NAMD/2.11-multicore
View Pyrazole.inp
#! MP2 cc-pVDZ gradient for the H2O molecule.
molecule pyr {
0 1
N 1.03435 0.06135 0.04027
C 2.37479 0.14799 0.05192
C 3.21797 1.23076 0.05844
C 4.51299 0.67646 0.06886
N 4.49937 -0.65931 0.06942
View GetResiduesWithinNang.py
import numpy as np
import mdtraj as md
import matplotlib
import pandas as pd
def GetResiduesWithinNang(traj,radius=20):
top = traj.topology
ligand = top.select('resname JLJ')
prot = top.select("protein and mass>2")
#def SelectWithinNangs(prot,ligand):
View atom_pair_distances.py
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"])
View NAMD_GPU_CPU_job.sh
#!/bin/bash
#SBATCH --partition=gpu
#SBATCH --job-name=install
#SBATCH --ntasks=10 --nodes=1
#SBATCH --mem-per-cpu=6000
View SPE.in
units real
atom_style full
dimension 3
boundary p p p
pair_style lj/cut/coul/cut 20.0 20.0
pair_modify mix geometric
bond_style harmonic
View orca.inp
! HF SVP OPT
! CPCM(Water)
%output
Print[ P_Hirshfeld] 1
end
* xyzfile 0 1 mobley_1323538.xyz
View ModifZmat.py
import pandas as pd
import numpy as np
import os
import sys
fname = sys.argv[1]
def ZmatRead(filename='OPLS_TMA.z'):
zmat_part = []
add_bonds = []
View CreatePSF.tcl
## Written by Leela S. Dodda, leela.dodda@yale.edu
##COMMAND TO RUN THE CODE
##VMD -dispdev text -e CreatePSF.tcl
mol load pdb protein_clean.pdb
## Change the pdb file name to one of your choice
set protein [atomselect top protein]
set chains [lsort -unique [$protein get pfrag]]
foreach chain $chains {
set sel [atomselect top "pfrag $chain"]
$sel writepdb myfile_frag${chain}.pdb
View combineGro_prot_lig.py
## Usage: python combineGro_prot_lig.py protein_clean.pdb UNK.pdb
import sys
import os
def GetCharge():
lines = open('LOG_CHARGE').readlines()
charge = []
for line in lines:
if 'System has non-zero total charge' in line:
charge.append(float(line.split()[-1]))