[gmx-users] fixing HOH

[Anton Feenstra]

Alan Wilter Sousa da Silva wrote:

> Hi List!
> 
> I was wondering if pdb2gmx is able to rebuild missing Hidrogens of
> structural waters from cristallographic PDB.

Yes - in principle. There should be a .hdb entry for 'HOH' or something
similar in the ff*.hdb file for whatever ff you use. If not, you can
easily steal it from the ffgmx.hdb, after taking proper care of atom
names.

> Maybe does it depends on PDB atom nomenclature?

It probably does, check the .hdb entry.


-- 
Groetjes,

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