[MMTK] modeling arbitrary structures

Konrad Hinsen hinsen@cnrs-orleans.fr
Tue, 7 Aug 2001 11:04:53 +0200


> thinking that there is little support for this sort of thing? I'd
> like to be able construct Molecule objects directly from structure
> files, do some manipulations on them, and then write them back out
> into a file -- the usual routine. What I'm wondering is if MMTK is
> too tied to the Database method of constructing molecules to easily
> support the reading of arbitrary structure files? I realize that one

It is possible to have molecule objects that are not associated with a
database file. Peptide chains are a good example. However, there is no
support at the moment for building molecules in any other way, with
the exception of the specialized code for biomolecules (peptide and
nucleotide chains).

I suppose that for someone familiar with structure files etc., it
would be easy to add the necessary code to MMTK. However, I have no
experience at all with this, so no promises... One problem I see is
force field parameters. If you have nothing but a structure file, and
want to calculate energies, you need an algorithm to deduce force
field parameters, or a force field that doesn't need any non-obvious
parameters.

> can read PDB files directly, but even in that case (if I read the
> code correctly) there is still a pretty heavy reliance on Database
> definitions. I'm hoping that this is really not a problem at all and

If you have a PDB file containing "unknown" residues, MMTK can still
construct AtomCluster objects from them. You can do all kinds of
geometrical calculations with them, but no energy-based calculations.

Konrad.
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