[gmx-users] Problem with Prdrg with NR5

[Daan van Aalten]

That is an incorrect statement - implcicit hydrogens are used only for
APOLAR hydrogens. All hydrogens in the input drawing are discarded and
PRODRG uses a set of rules for dtermining which atom show have polar
hydrogens added. In case of aromatic cyclics containing nitrogens this is
not a trivial problem and PRODRG does indeed not get it always right.

Daan

On Tue, 12 Mar 2002, Anton Feenstra wrote:

> 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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> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust RCD Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O