[gmx-users] Phenol topology

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Nov 28 22:25:00 CET 2005

Hi Deepa Rajamani,

What about basing the topology on the side chain of a tyrosine?


On 11/28/05, deepa rajamani <deepsri at bu.edu> 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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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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