[MMTK] Change of amino acid definition file

Konrad Hinsen hinsen@cnrs-orleans.fr
16 Oct 2001 14:32:11 +0200


Berit Hinnemann <Berit.Hinnemann@fysik.dtu.dk> writes:

> If I then change the file "glycinexx" (I am changing the partial
> charges) and then ask for the energy, the changes are not taken into
> account, so the file is apparently not reread. I have tried to create

Right. For efficiency reasons, the database files are read only once
and the information is cached.

> I am also making changes in the AMBER parameter modification file, while
> MMTK is running, and this file is read whenever I create the universe
> new. When is the amino definition file actually read and how could I
> enforce it to be reread?

The amino acid definition is read when it is needed for the first time.
The same goes for the main Amber parameter file, only the modification
files are read each time a force field object is created.

I am not sure that rereading the file is a good idea. Currently the
name of some group or molecule is a unique specification. If you
permit that molecules or groups with the same name might in fact be
completely different, then some algorithms might break down.

Why don't you use a new filename for each modification, and then call
defineAminoAcidResidue() again to attach it to the same codes?
Or if all you need to modify is partial charges, why don't you
simply assign charges to the atoms after the object is created?
A simple

      atom.amber_charge = 0.7

will do the trick.

Konrad.
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