[MMTK] Normal modes -defaulty adds hydrogen to pdb

Konrad Hinsen research at khinsen.fastmail.net
Wed Dec 12 15:23:13 UTC 2012

Mohan maruthi sena writes:

 >              I want to calculate normal modes for a protein. The
 > mmtk universe.protein routine by default  adds hydrogen to pdb. I
 > dont want hydrogens to be added to pdb. I just want normal modes of
 > the protein without hydrogen. How can I do this  using MMTK?

MMTK adds hydrogens by default because the Amber forcefield requires
hydrogens. You can build a model without hydrogens by adding


to the arguments of Protein() or PeptideChain(). However, you cannot
use the Amber forcefield with the resulting model, so you have to use
something else, such as the DeformationForceField.

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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