[MMTK] trouble of exporting cofactor to pdb file

Konrad Hinsen research at khinsen.fastmail.net
Fri Mar 25 06:48:20 UTC 2011

Tao-wei Huang a écrit :

> 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:


> universe = InfiniteUniverse(Amber94ForceField())
> universe.protein = Protein('some.pdb')

This is where your cofactor disappears. The Protein constructor is a 
simple but limited way to define proteins in MMTK: it takes the peptide 
chains from a PDB file and assembles them into a protein, adding 
hydrogens and disulfide bridges, but it throws away everything from the 
PDB file that is not a peptide chain.

There are more flexible ways to select parts of a PDB file for inclusion 
into your system, but they require some more effort as well. Have a look 
at class PDBConfiguration, and at the example scripts that use it.

Note also that if your cofactor is a molecule unknown to MMTK, you must 
first write a molecule definition file and put the Amber force field 
parameters in there, before you can do energy minimization.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net

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