[MMTK] oing MD with crystallographic water molecules

Konrad Hinsen research at khinsen.fastmail.net
Fri Apr 9 09:16:34 UTC 2010


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> From: mmtk-bounces at starship.python.net
> Date: 9. April 2010 05:11:35 MESZ
> To: mmtk-owner at starship.python.net
> Subject: Auto-discard notification
> 
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> From: prabhakar g <prabha.iisc at googlemail.com>
> Date: 9. April 2010 03:58:14 MESZ
> To: mmtk at starship.python.net
> Subject: Doing MD with crystallographic water molecules
> 
> 
> Dear all,
> 
> I am new to MMTK and to MD as well, I want to do MD simulation of a PDB structure along with its crystallograpic water molecules.  I tried running the scripts in the example folder. it worked out well for the protein molecules without any crystallograpic water.  Here is what i did
> 
> I used the scripts 
> construct.py for adding hydrogens
> protein.py for  doing the equilibration and production
> restrat.py for running more production steps.
> 
> but when i used the construct.py  along with water molecules
> 
> #! /usr/bin/python
> from MMTK import *
> from MMTK.PDB import PDBConfiguration
> from MMTK.Proteins import PeptideChain, Protein
> configuration = PDBConfiguration('6LYZ.pdb')
> chains = configuration.
> createPeptideChains()
> insulin = Protein(chains)
> insulin.writeToFile('bala1.pdb')
> 
> the output file did not contain any water molecules in it. 
> could anyone  suggest how to include waters...
> 
> Moreover I would like to do MD with the crystallographic water molecules using the periodic boundary conditions. Is this reasonable, hope someone give suggestions.
> 
> Sincerely
> prabha
> 
> 

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