[gmx-users] addition of all hydrogens in pdb2gmx

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 14 19:06:46 CEST 2008

Hi Sridhar,

pdb2gmx adds all hydrogens _according to the force field definition_
(and a database file describing how to add which hydrogen where).
If you want to have all hydrogens "satisfying the valencies", you need
to choose a force field that includes them, i.e. an all-atom force
field. Maybe it would be good to read a bit more about united atom /
all atom force fields and such.



On Thu, Aug 14, 2008 at 5:56 PM, sridhar acharya <sridharfirst at gmail.com> wrote:
> Hi,
> The manual says, pdb2gmx adds all hydrogens, including those for carbons.
> But I could not find the output gro file to contain all the hydrogens
> (especially for carbons) satisfying all the valencies. Is there any option
> that I may be missing?
> thanks,
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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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