[MMTK] trouble of exporting cofactor to pdb file

Tao-wei Huang yelvergm at gmail.com
Fri Mar 25 01:51:13 UTC 2011


Hi,

I want to perform energy minimization for one protein. But the protein
contains some cofactor and I cannot find it in the exported pdb file.
Can anyone help me to fix this problem? I am quite new to the package.
I tried to read the example codes but still unable to identify the
reason.

My code is as following:
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.Minimization import SteepestDescentMinimizer
from MMTK.Trajectory import StandardLogOutput

# Construct system
universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('some.pdb')

# Minimize
minimizer = SteepestDescentMinimizer(universe)
##                                       actions=[StandardLogOutput(50)])
minimizer(steps = 10)

#output
universe.protein.writeToFile('toy.pdb')



Cheers,
Tao



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