[MMTK] all atom model for lipdis

khinsen@cea.fr khinsen at cea.fr
Tue Jan 10 09:45:09 CET 2006


On 03.01.2006, at 00:50, andruty at op.pl wrote:

> Is it possible to build all atom structure  from united atom  model  
> for lipid molecules ( I have got   DHCP and DMPC  ua definition  
> files ) using MMTK ?
> Does MMTK have any  function that adds hydrogens to molecules like  
> lipids in the same way as 'configuration.createPeptideChains()'  
> makes it for proteins?

Yes. MMTK can add missing hydrogen atoms to a rather large class of  
molecules, which includes lipids. However, you need to have a  
database file for the fully hydrogenated lipid. Since the default  
database doesn't have any lipids at all, you will have to write that  
file yourself. Once you have done that, you construct a lipid  
molecule with just the positions of the non-hydrogen atoms and then call

	lipid_molecule.findHydrogenPositions()

Konrad.
--
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Konrad Hinsen
Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
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