[gmx-users] AMBER (parm96) force field & hydrogen/termini database

[Anton Feenstra]

Hi All,


First of all, sorry for the cross-post, but Filip Ryjacek wrote a 
message somewhere last year to gmx-users about porting AMBER ff
to Gromacs. But imho a discussion on that belongs in the gmx-dev
list. So, that's why...

Anyway, Filip Ryjacek mentioned work on a topology/coordinate
converter he is developing. I am in the process of writing a set of
scripts (which could easily be 'ported' into C) that read the parm*.dat
and all*.in parameter files from Amber and write the corresponding
Gromacs versions (*bon.itp *nb.itp *.tdb *.hdb *.rtp *.atp). My feeling
is that we sh/could benifit mutually. Also, I would assume more people
are potentially interested in this.

Currently I am at the stage that I 'only' need the hydrogen and termini
databases to work out. Especially the hydrogen database is non-trivial
since it involves quite some 'chemical' knowledge, i.e. what hydrogens
to add where and how. I am at the moment wondering whether it would
be easier to do the conversion, or to eliminate the .hdb altogether and
put the 'intelligence' part into pdb2gmx directly, since everything 
should in principle be deducible from the topologies as described in
the .rtp (in that respect, the Amber files are set up more conveniently,
since for each residue is described also as a Z-matrix, which enables
any atom coordinates to be generated if needed).

The terminus database is more or less trivial, except for the fact
that in Gromacs it is implemented in quite a different way (Gromacs
stores the possible modifications, Amber stores a separate set of all
residues for when they occor at the C or N terminus).

Any ideas, hints, comments, or cooperation appreciated...!


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)  |
|________|___________________________________________________________|