Thank you for your advice!<br>I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and probably it would complain also for ffG43a2x-c.tdb. Here, also the fields gd_* don't match. Is there the way to use the existing topologies with another gromos force field instead of reformatting all the ffG43a2x* files? What about the "atomtype 'CA' not found!" error?<br>
<br><div class="gmail_quote">On Fri, Mar 21, 2008 at 12:57 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">Quoting Chiara Parravicini <<a href="mailto:parravicini.chiara@gmail.com">parravicini.chiara@gmail.com</a>>:<br>
<br>
> Dear gromacs users,<br>
><br>
> I would like to perform simulations of a protein embedded in popc, using a<br>
> force field of the gromos series and I downloaded popc.pdb, popc.itp,<br>
> lipid.itpa and the force field ffG43a2x extended for lipids.<br>
> Looking throughout the archive I found different suggestions, but none of<br>
> them help me to successfully perform my simulations:<br>
><br>
> - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I get<br>
> this error:<br>
><br>
> Fatal error:<br>
><br>
> Error in hdb file ffG43a2x.hdb:<br>
><br>
> Wrong number of control atoms (2 iso 3) on line:<br>
><br>
> 1 1 N -C CA<br>
<br>
</div>Right; I think the format of the .hdb file changed somewhere along the way, and<br>
ffG43a2x is formatted in the old style. What pdb2gmx is complaining about is<br>
that it thinks it is trying to add an atom named 'N', with reference atoms of<br>
-C and CA. Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will see<br>
the difference. The first atom specified must be the name of the hydrogen atom<br>
you wish to add, so that line should be something like:<br>
<br>
1 1 H N -C CA<br>
<br>
For more on .hdb files, read the manual, section 5.5.2.<br>
<br>
-Justin<br>
<div class="Ih2E3d"><br>
><br>
> - If I manually write a topology file for the ffG43a2x force field and<br>
> submit it to grompp to write a .tpr, I get this error:<br>
><br>
> Fatal error:<br>
> Atomtype 'CA' not found!<br>
><br>
> In the topology file I included both lipid.itp and popc.itp, and I<br>
> commented the following lines in the lipid.itp file as suggested:<br>
><br>
> [ defaults ]<br>
><br>
> 1 1<br>
><br>
> - I also tried to add the different sections [ atomtypes ], [ pairtypes ],<br>
> etc... of the lipid.itp files to ffG53a5* files, but I still get the error:<br>
><br>
> Atomtype 'CA' not found!<br>
><br>
> Does anybody know what I miss? Is there a way to resolve this problem and<br>
> use popc with ffG53a5 or ffG43a2x?<br>
><br>
> All comments are very appreciated!<br>
> Thanks in advance!<br>
><br>
> Chiara<br>
><br>
<br>
<br>
<br>
</div>========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br>
<br>
========================================<br>
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