[MMTK] Re: Intramolecular interactions

khinsen at cea.fr khinsen at cea.fr
Thu Jul 21 09:23:53 CEST 2005


On 20.07.2005, at 21:08, Matias Saavedra wrote:

> Hi Konrad... I need for a program i'm creating, to
> have the information of all the interactions that are
> established in a given protein structure
> (electrostatic, hydrophobic, disulfur bonds, van der
> waals etc..).
>
> I think that the force fields have to take into
> account that information, so is it possible to access
> it in MMTK?

Yes, but the force field internals are undocumented, because they are  
specific to each force field. Moreover, the data is stored in a way  
that is convenient for force field evaluation, but not necessarily for  
retrieving the data in any other way.

> I need to know which atom from which residue interact
> with other atom from other residue, and the kind of
> interaction... that for all the interactions inside
> the protein.

Such complete information is not stored anywhere in MMTK. Interaction  
lists exist only for the bonded interactions (bond, angle, and dihedral  
terms), and those are easy to retrieve. For nonbonded interactions,  
only the atomic parameters are stored, plus separately a nonbonded list  
which provides efficient access to all pairs of atoms within the  
largest cutoff being used. You can use that list for generating a list  
of all interactions, but it requires some additional work.

The code to look at for inspiration is in MMTK.ForceFields.MMForceField  
and in MMTK.ForceFields.EnergyEvaluator.

Konrad.
--
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Konrad Hinsen
Laboratoire Leon Brillouin, 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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