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Leela Dodda leelasd

  • Yale University
  • United States
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@leelasd
leelasd / ASE_NVT.py
Created Mar 20, 2019
NVT of molecule with DFTB using ASE
View ASE_NVT.py
"""Demonstrates molecular dynamics with constant energy."""
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
from ase.md.langevin import Langevin
from ase.calculators.dftb import Dftb
from ase.optimize import QuasiNewton,fire,gpmin,mdmin,LBFGS
from ase.io import write,read
from ase.build import molecule
@leelasd
leelasd / ASE_NVE.py
Created Mar 20, 2019
ASE NVE MD simulation of Organic Molecule
View ASE_NVE.py
"""Demonstrates molecular dynamics with constant energy."""
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
from ase.calculators.dftb import Dftb
from ase.optimize import QuasiNewton,fire,gpmin,mdmin,LBFGS
from ase.io import write,read
from ase.build import molecule
from rdkit import Chem
@leelasd
leelasd / ASE_Minimizers.py
Created Mar 20, 2019
ASE DFTB minimization Algorithms
View ASE_Minimizers.py
from ase.calculators.dftb import Dftb
from ase.optimize import QuasiNewton,fire,gpmin,mdmin,LBFGS
from ase.io import write,read
from ase.build import molecule
from rdkit import Chem
from rdkit.Chem import AllChem
from ase.optimize.minimahopping import MinimaHopping
from ase import *
from ase.optimize.basin import BasinHopping
@leelasd
leelasd / AnalyseTrajCluster.py
Created Feb 13, 2019
Clustering Trajectory with msmbuilder and mdtraj
View AnalyseTrajCluster.py
import numpy as np
import mdtraj as md
import matplotlib
matplotlib.use('Agg')
import random
import matplotlib.pyplot as plt
import pandas as pd
import argparse
d = """
@leelasd
leelasd / split_complex_v2.py
Created Nov 29, 2018 — forked from PatWalters/split_complex_v2.py
An improved script to extract a ligand from a protein-ligand complex and assign bond orders
View split_complex_v2.py
#!/usr/bin/env python
import sys
from prody import *
from rdkit import Chem
from rdkit.Chem import AllChem
from io import StringIO
import pypdb
View AnalyseNAMDMetaDwithVMD.tcl
mol new "../../ionized.psf"
mol addfile "../1KLM_metad.dcd" waitfor all
cv molid 0
#cv configfile "MetaDynamics_wRMSD.in"
cv configfile "TTT.in"
set numFrames [ molinfo 0 get numframes ]
for { set frame 0 } { $frame < $numFrames } { incr frame } {
animate goto $frame
cv frame $frame
cv colvar "CNUM" update
@leelasd
leelasd / competitive_binding.py
Created Sep 12, 2018
Equilibrium Concentrations of two ligands in case of Competitive binding
View competitive_binding.py
# -*- coding: utf-8 -*-
"""Competitive Binding.ipynb
Created on Sep 11 15:40:05 2016
@author: Leela S. Dodda leela.dodda@yale.edu
@author: William L. Jorgensen Lab
Automatically generated by Colaboratory.
Original file is located at
https://colab.research.google.com/drive/1xm_e38URAOk4Aspxffkupbm_zMyKcFxv
"""
@leelasd
leelasd / MetaDynamics_CreatePSF.tcl
Created Aug 27, 2018
Create PSF file and other things using the following script
View MetaDynamics_CreatePSF.tcl
## vmd -dispdev text -e MetaDynamics_CreatePSF.tcl
mol load pdb protein_clean.pdb
set protein [atomselect top protein]
set chains [lsort -unique [$protein get pfrag]]
foreach chain $chains {
set sel [atomselect top "pfrag $chain"]
$sel writepdb myfile_frag${chain}.pdb
}
### Split the PDB file into segments and then create a over all psf/pdb file
package require psfgen
@leelasd
leelasd / Mols2SDF.py
Created Jul 23, 2018
Write SDF file from bunch of mol files
View Mols2SDF.py
import glob
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd
#csvs = glob.glob('CSVS/*.csv')
csvs = open('List','r').readlines()
mol_list = ['MOLS/'+m[5:-4]+'mol' for m in csvs]
#fnames = pd.read_csv('ListMols',header=None)
#fnames.columns = ['MOL'],sanitize=False,strictParsing=False
@leelasd
leelasd / ORCA_CPU_Grace.sh
Created Jul 10, 2018
ORCA SLURM JOB SCRIPT
View ORCA_CPU_Grace.sh
#!/bin/bash
#SBATCH --partition=scavenge
#SBATCH --job-name=HIV
#SBATCH --ntasks=1 --nodes=1
#SBATCH --mem-per-cpu=6000
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