[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.

Groeten, David.
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

More information about the gromacs.org_gmx-developers mailing list