[gmx-users] ffamber99p -- .hdb editing

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Apr 23 21:05:22 CEST 2007

Hi Stan,

> I suggest you may find solution outside Gromacs. Use Pymol or other
> software to simply add hydrogen. Check it (usually they will ignore some
> double bonds) and put it back to GROMACS.

This is not encouraged and likely would not solve your problems (sorry
Yang Ye).
The .hdb format does not depend on the force field, and I would
strongly suggest to follow Marks advice and read Chapter 5. But, in
addition to that, note that it comes quite strict with atom names and
such. The .pdb/.gro file and the .rtp file have to match, and also the
hydrogen names have to match. If they're in the .pdb file, they'll
have to have the same name as in the .rtp file. The names in the .hdb
file also have to match those in the .rtp file, but there you have to
be aware that pdb2gmx will add the numbers automatically. If this
doesn't make much sense..., go read Chapter 5 of the manual thoroughly
and have a good look at ATP (e.g.).



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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