Hello, I am trying to perform MD simulation for the protein-ligand system and I got this after Minimization. I used openMM for minimization and I used ambertool for protein-ligand parameterization
Any idea why this happened ?! the code used for minimization is :
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout, argv
temperature = 298.15 * kelvin
prmtop = AmberPrmtopFile('prot_LIG.prmtop')
inpcrd = AmberInpcrdFile('prot_LIG.inpcrd')
system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
########## This is to apply constraints on the backbone
################################################################
integrator = LangevinIntegrator( temperature, 1 / picosecond, 0.0002 * picoseconds)
platform = Platform.getPlatformByName("CUDA")
properties = {"CudaPrecision": "mixed"}
simulation = Simulation(prmtop.topology, system, integrator, platform , properties)
simulation.context.setPositions(inpcrd.positions)
if inpcrd.boxVectors is not None:
simulation.context.setPeriodicBoxVectors(*inpcrd.boxVectors)
simulation.minimizeEnergy()
position = simulation.context.getState(getPositions=True).getPositions()
energy = simulation.context.getState(getEnergy=True).getPotentialEnergy()
app.PDBFile.writeFile(simulation.topology, position, open('opt_prot.pdb', 'w'), keepIds=True)
print('Energy at Minima is %3.3f kcal/mol' % (energy._value * KcalPerKJ), file=open("energy.txt", "a"))
may be your PBC conditions are not stringent. check box size or issue might be with protein centering.
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