[MMTK] Amber parameters for ligands

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Nov 19 17:05:54 UTC 2008

On Nov 19, 2008, at 17:46, Lars Skjærven wrote:

> so the following would be the way to go?
> for each atom in ligand:
>      atom.amber_charge = 'charge_from_amber_prep_file'
>      atom.amber_atom_type = 'atom type from amber prep file'
> Would MMTK then know the topology, and thus we would be "set to go"
> for minimization?

No, you need to tell it where the bonds are. However, you can create  
the bond structure through a MoleculeFactory, that's why I wrote that  
a database file is not strictly necessary. It may well be the easiest  
way for you, of course.

> A more general way would be cooler though. What would I need in order
> to build a script that automatically builds MMTK database files from
> amber topology files ? Will it not be rather straight forward? I guess
> there is a reason for why you did not do it fully automatically, so
> there is something I don't see yet.

For a single molecule, the conversion would be rather straightforward  
and could very probably be done automatically by a script. What I  
converted many years ago was the complete database of amino acid and  
nucleic acid residues. I had to do the mapping from Amber residue  
names to MMTK group names manually, which is why the conversion was  
not fully automatic.

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

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