[gmx-users] Hydrogens moving inside ring?

[Daan van Aalten]

Hi Joanna

Is this a hand made or PRODRG-grown topology? If the former try the
latter. If the latter, alert the authors of the former!

cheers

Daan

On Tue, 16 Sep 2003, Joanna Bailey wrote:

> I am running a molecule which includes a triazine ring, where two of the
> nitrogens have hydrogens and two of the carbons are part of carbonyl
> groups.  When I run the energy minimisation, which converges, the hydrogens
> end up inside the ring with the ring remaining flat. Obviously there is
> something very wrong, I have checked the dihedrals both improper and proper
> and the bond angles, all seems fine. Is there anything else anyone could
> suggest could be the problem? Thank you.
>
> Jo
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA 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

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