feenstra at chem.vu.nl
Mon Jul 21 16:55:01 CEST 2003
> Dear Anton Feenstra
> I have got files of ffamber...from /gmx/src/contrib/scripts/ in CVS.
> I have tow questions:
> 1-Are these files correct?
In principle: no, since I have not tested them. In practice, nearly,
since I did this rather systematically and automated. You should
check for yourself, I'm afraid, since I never got to really use them
> 2-If I want produce a consistent topology file with amber force field,
> what should I do?
If you have used the scripts with your amber forcefield files of
choice as input, you should have (IIRC) the appropriate Gromacs
files, i.e. at least *nb.itp, *bon.itp, *.rtp and *.atp. That
should be enough to use pdb2gmx, but be prepared to encounter
all sorts of problems in the generated files.
Seeing that the group of Vijay Panda (Stanford U, IIRC), has
been implementing Amber ff into Gromacs also, I have stopped
any work on these scripts, and am not likely to provide you
with any support...
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Room P275 Tel: +31 20 44 47608 Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "Engage" (J.L. Picard) |
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