[gmx-users] Phenol topology

MGiò magiofer at gmail.com
Tue Nov 29 10:47:05 CET 2005


I had the same problem with an aromatic ring in oestradiol, which I solved
defining explicitly all the ring hydrogens and defining the out-of-the-plain
and the proper dihedral angle for each of them. oh, remember that GROMACS
needs the internal proper angles of the ring defined with function 2, like
improper dihedral angles, or it won't keep them plate!

good luck!


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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