[gmx-users] FF & LIGANDS's topology

[Anton Feenstra]

Arturas wrote:

> Hello , gmx-users,
> 
> I do modeling on protein-ligand complex and got error that my iginad's
> atoms "has mass 0".
> 
> Similar error was found in mailing list. I have checked the thread
> "GROMOS96 and protein-ligand complex" posted almost a year ago in the
> gmx mailing list. However i didn't found the summurising answers how
> to treat prepared ligand topology with PRODRG applying to FF43a1
> model.
> 
> In the mailing list, some (David van der Spoel) advised to add mass
> column to ligand's topology file, but some (Anton Feenstra) said that
> it is a bad way as "It sounds as if you're mixing (parts of)
> forcefields ...".

I remember saying that, but certainly not in this context. As David
said, you need to *convert* a Gromacs forcefield to Gromos (ffG43a),
and part of that is adding explicit masses in the topology.


-- 
Groetjes,

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