Hi!<br>
<br>
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!<br>
<br>
good luck!<br>
<br>
Magiofer<br><br><div><span class="gmail_quote">On 11/28/05, <b class="gmail_sendername">deepa rajamani</b> <<a href="mailto:deepsri@bu.edu">deepsri@bu.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>I have problems creating phenol topology file. I created the top file from<br>PRODRG server, but when I use the file and convert the trajectories back<br>to pdbs, the carbons are not aromatic but they look like cyclohexanol.
<br><br>Is there a way to correctly assign aromatic carbons in the topology files,<br>I followed the atom type specified in the .atp file and still have the<br>same problem.<br><br>Deepa Rajamani<br>_______________________________________________
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