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leelasd/serial_parmed.py

Created October 15, 2017 04:06
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Serialize Parmed System
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serial_parmed.py
structure = parmed.openmm.topsystem.load_topology( pdbfile.topology, system, pdbfile.positions)
structure.save('system.prmtop', overwrite=True)
structure.save('system.crd', format='rst7', overwrite=True)
parm = parmed.load_file('system.prmtop', 'system.crd')
ambersys = parm.createSystem(nonbondedMethod= app.NoCutoff, constraints = None, implicitSolvent = None)
from simtk.openmm import XmlSerializer
serialized_system_amber = XmlSerializer.serialize(ambersys)
outfile = open('amber_system.xml','w')
outfile.write(serialized_system_amber)
outfile.close()
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