[gmx-users] Phenol topology

[Daan van Aalten]

Dear Deepa

This does not sound good!

Can you give us the exact input (did you use a PDB file/drawing?) you give
to the PRODRG server so that we can reproduce this and we will investigate
and report back.

Daan

On Mon, 28 Nov 2005, deepa rajamani wrote:

> Hi,
>
> I have problems creating phenol topology file. I created the top file from
> PRODRG server, but when I use the file and convert the trajectories back
> to pdbs, the carbons are not aromatic but they look like cyclohexanol.
>
> Is there a way to correctly assign aromatic carbons in the topology files,
> I followed the atom type specified in the .atp file and still have the
> same problem.
>
> Deepa Rajamani
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Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
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