Hi Deepa Rajamani,<br><br>What about basing the topology on the side chain of a tyrosine?<br><br>Tsjerk<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>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>