Hi Andrea,<br><br>I would suggest making a building block in the ff*.rtp file. Copy the entry for aspartic acid, and rearrange such that the connection runs through the side chain rather than through the backbone. <br><br>
In addition, you can better use one of the GROMOS force fields, OPLS or Amber; check posts on the gmx force field (and why not to use it for MD simulation) in the archive.<br><br>Best regards,<br><br>Tsjerk<br><br><div><span class="gmail_quote">
On 2/21/06, <b class="gmail_sendername">andrea spitaleri</b> <<a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</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;">
Dear all,<br>I have a small cyclic peptide (5 aa) and one aminoacid is a non-natural<br>aa, isoaspartic acid (isoASP). In order to create a topology file,<br>I was thinking to follow to routes:<br>1. create two different itp files, one for standar aa and one for the
<br>isoASP and then include them in the top file. In this case, how can I<br>define the bond between isoASP and the rest of aa in the itp files?<br>or<br>2. edit the ffgmx.* files in order to add also this isoASP<br>I am not aware of other way to carry out.
<br><br>Any other suggestions are welcome,<br><br>Regards,<br><br>andrea<br><br><br>--<br>-------------------------------<br>Andrea Spitaleri<br>Dulbecco Telethon Institute<br>c/o DIBIT Scientific Institute<br>Biomolecular NMR, 1B4
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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>