[gmx-users] Problem with Prdrg with NR5

[Anton Feenstra]

xmluo wrote:
> 
> Dear Gromacs users,
> 
> I encounter a problem while using Prodrg to make Gromacs top file.
> Hydrogen atom attached to nitrogen in the following molecule
> 
> C===C
> |    \
> |     N-H
> |    /
> C===C
> 
> was deleted, and the nitrogen atom was asigned with type NR5.
> Can someone help me? Thanks.

I think PRODRG only supports united atoms (i.e. implicit hydrogens).
IMO that is a missing feature. Nevertheless, in this case it would
be trivial to add the missing hydrogen by hand. Alternatively, you
might add a Carbon atom in stead of the Hydrogen, feed that to
PRODRG, and modify the Carbon back to hydrogen yourself, and also
fix the atomtype of the Nitrogen (which probably depends on how many
carbons are bound to it).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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