Dear Leila,<div><br></div><div>Consider reading all about ACPYPI at <a href="http://acpypi.googlecode.com">acpypi.googlecode.com</a>, specially the wiki pages. Although you may not be interested in topology generation for ligands, there's there important information about how to run amber force fields in Gromacs environment.</div>
<div><br></div><div>And review carefully your ffamber installation. It looks I had some similar issues in the past and although I never figured out what was the cause, a simply careful reinstallation of ffamber solved the problem.</div>
<div><br></div><div>And if using amber force field, consider registering yourself at amber mailing list (<a href="http://ambermd.org">ambermd.org</a>). I am suggesting that because as far as I know from literature amber99sb is the most advanced force field from amber, yet the year, but read:</div>
<div><br></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica">Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. Compar- ison of multiple amber force fields and development of improved protein backbone parameters. Proteins- Structure Function and Bioinformatics 65, 3 (NOV 15 2006), 712–725.</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Helvetica"><br></p><div class="gmail_quote">However, I understand you want to do nucleic acids simulation rather than proteins, so milage here is low and for that I suggested also the amber mailing list.</div>
<div class="gmail_quote"><br></div><div class="gmail_quote">I hope it may helps.</div><div class="gmail_quote"><br></div><div class="gmail_quote">Alan</div><div class="gmail_quote"><br></div><div class="gmail_quote">On Sat, Nov 21, 2009 at 11:00, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Send gmx-users mailing list submissions to<br>dear Mark<br>
<br>
your opinion is right [residue number 1 is NGLY in pdb file but residue<br>
number 1 is GLY in warning].<br>
<br>
howbeit, what work should I do?<br></blockquote><div> </div></div>-- <br>Alan Wilter Sousa da Silva, D.Sc.<br>PDBe group, PiMS project <a href="http://www.pims-lims.org/">http://www.pims-lims.org/</a><br>EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK<br>
+44 (0)1223 492 583 (office)<br>
</div>