[gmx-users] PRODRG with all hydrogens

[Anton Feenstra]

Markus O Kaukonen wrote:
> Dear All,
> 
> Is there a PRODRG-like way to generate hydrogens and
> topology file automatically for Gromacs (from .pdb file)
> with ALL hydrogens explicitly
> and not just polar H's (as PRODRG gives it).

For proteins, ffgmx2 does it. The program 'protonate' will accept
a structure (or trajectory) and uses the ffgmx2.hdb descriptions
to add all hydrogens. This may fail if atom names don't match, but
I've successfully used it on Gromacs/G43a1 generated trajectories.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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