[gmx-developers] Re: [gmx-users] AMBER (parm96) force field & hydrogen/termini database
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 3 02:20:48 CEST 2002
On Thu, 2 May 2002, Anton Feenstra wrote:
>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...!
First of all Erik L. has probably done most of this stuff recently too,
and also for other force fields. Anyway, most hdb information is in the
ffgmx2.hdb I would think.
Secondly all databases will be obsolete *real soon now* when we move to
the XML format. This will be much more general and simpler to use, but it
still requires some (quite a bit) of coding. Check the *dtd and *xml files
in the share/top CVS directory. I will do some cleaning etc. next week.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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