[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

   model="no_hydrogens"

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.
-- 
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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
http://dirac.cnrs-orleans.fr/~hinsen/
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