[gmx-users] Phenol topology

deepa rajamani deepsri at bu.edu
Mon Nov 28 21:47:43 CET 2005


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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