[gmx-developers] Amber to Gromacs forcefield conversion

[Anton Feenstra]

Hi Developers,


I've just now commited my amber2gmx forcefield comversion scripts
to the CVS in src/contrib/scripts. IN addition to the amber2gmxff
and amber2gmxrtp scripts, I also committed the converted files in
Gromacs format (ffamber* files and some), and two additional scripts.
One sorts .hdb files alphabetically, to make comparisons easier
(e.g. between ffamber.hdb and ffgmx2.hdb). The other comments out the
[ pairs ] section in a .top file, since this is still not in working
order in the ffamber forcefield as it is converted now by the scripts.

The amber2gmx* scripts display explanatory text when run without
arguments, that is supposed to be clear enough to get you going.
First run amber2gmxff (forcefield) and then amber2gmxrtp (building
blocks). For amber2gmxrtp you can convert any number of Amber all*.in
files in one go (e.g. normal and terminal amino acid residues, and 
nucleic acids, i.e. 4 Amber files), they will be put into one large 
.rtp file.

Known bugs and problems at this moment are: 
- pairs, grompp says: no defaults. That is reasonable, since no
  pairtypes are defined yet. I have to look up how they are defined
  in the Amber ff. I think it is simply a scaling with respect to
  the normal LJ parameters.
- impropers: a trial EM run on a peptide results in distorted
  geomoetry. Nothing definite yet, but it seems the impropers are off.

So, please, try it. Don't expect anythin to work, but shoot at it
and tell me what you think about it... Thanks in advance! ;-)

-- 
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   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Breaking the Law, Breaking the Law" (Judas Priest)       |
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