[MMTK] solvation and saving to PDB file

prabhakar g prabha.iisc at googlemail.com
Fri Feb 18 07:42:06 UTC 2011

Dear Users,

Am trying to solvate a protein molecule, equilibrate it and save the
equilibrated coordinates into a PDB format file.
I used the example solvation.py script to solvate and equilibrate the
molecule.  Solvation and equilibration is working well. Now while converting
the equilibration.nc trajectory file into  PDB form I used the below example

from MMTK import *
from MMTK.Trajectory import Trajectory
from MMTK.PDB import PDBConfiguration, PDBOutputFile

trajectory = Trajectory(None, "equilibration.nc")
universe = trajectory.universe

for i, conf in enumerate(trajectory.configuration):
    universe.writeToFile("conf%d.pdb" % i, conf)

Running this script gives the below error and  the system hangs

*** glibc detected *** python: malloc(): memory corruption: 0x0a47d4f8 ***

Hope somebody could help

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