Dear Alan,<br>if I completely understood how acpypi works, it seems that it generates the topology parameters from the pdb file of the molecule.<br>But the problem is that I have the topology parameters (my angles, bond distances and dihedrals) and want to implement them in Gromacs, so actually I want to set specific parameters' values in gromacs.<br>
<br>Carla<br><br><div class="gmail_quote">On Tue, Oct 20, 2009 at 5:16 PM, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Carla,<br>
<br>
Let me suggest you the wikis at <a href="http://acpypi.googlecode.com" target="_blank">acpypi.googlecode.com</a>.<br>
<br>
And then let me ask why amber94 and not amber99sb? And why not trying<br>
acpypi in the link above as I guess it can do pretty much what you<br>
want with much less pain?<br>
<br>
Cheers,<br>
Alan<br>
<div><div></div><div class="h5"><br>
On Tue, Oct 20, 2009 at 15:55, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
><br>
> Hi everyone,<br>
> I'm using the amber94 force field in gromacs. I need to add topology of a<br>
> new molecule for my MD simulation.<br>
> I saw this line "propers treated as RBs in GROMACS to use combine multiple<br>
> AMBER torsions per quartet" in my ffamber94bon.itp file.<br>
> So it seems that I have to convert my proper dihedrals parameters into RB<br>
> parameters, in order to run my simulation.<br>
> Does anyone have an idea of how can I do this, to have the right parameters<br>
> for my molecule?<br>
><br>
> Thanks a lot<br>
><br>
> Carla<br>
<br>
</div></div>--<br>
Alan Wilter Sousa da Silva, D.Sc.<br>
PDBe group, PiMS project <a href="http://www.pims-lims.org/" target="_blank">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>
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