Hello Ragnarok,<div><br></div><div>I am the author of acpypi and I believe Mark's guessing right. I strongly suggest you to look my simple tutorial for some warnings about where to place correctly the entries for amberff in *.top file:</div>
<div><br></div><div><a href="http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs">http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs</a></div><div><br></div><div>In particular: "<strong>NB(1):</strong> <tt>#include "Ligand.itp"</tt> has to be inserted right after <tt>ffamber**.itp</tt> line and before <tt>Protein_*.itp</tt> line in <i>Complex.top</i>."</div>
<div><br></div><div>I intendo to update this tutorial for a more realistic situation (i.e., using PME for instance, etc.), but only in Jan when I intend to make an official release. I also suggest to use latest revision o acpypi since I updated that last week.</div>
<div><br></div><div>I also want people to know that I tested acpypi and ffAMBER for GMX 3.3.1 with GROMACS 4.0.2 and seemed to work like a charm.</div><div><br></div><div>Cheers,</div><div>Alan<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
Ragnarok sdf wrote:<br>
> I am trying to setup a simulation with a ligand and a protein using<br>
> ffamber99 forcefield. I have already generated the ligand's topology<br>
> file using acpypi and everything seems to be all right in the files<br>
> generated. However, while following the steps in the drug enzyme<br>
> tutorial provided in the gromacs' web site, after i add the ligand to my<br>
> protein's .gro file and edit the lines in my topology file to include<br>
> the ligand's topology, when i type the command editconf, my ligand<br>
> dissapears from my .gro file. The .gro generated from my original<br>
> ligand-protein complex.gro does not include my ligand coordinates<br>
> whatsoever.<br>
<br>
I'm guessing you've added your ligand to the end of the file, but not<br>
adjusted the total number of atoms at the top of the file.<br>
<br>
Mark<br>
<br></blockquote></div><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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