Hi Justin,<br><br>I did not mention that I am indeed trying run Gromacs implementing the MARTINI force field. I realize this is not as automatic as selecting other force fields in Gromacs using pdb2gmx. This issue has been previously discussed in:<br>
<br><a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg14945.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg14945.html</a><br><br>-Lili<br><br><div class="gmail_quote">On 25 March 2010 18:13, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
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<br>
<a href="mailto:rainy908@yahoo.com" target="_blank">rainy908@yahoo.com</a> wrote:<br>
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Dear GMX users,<br>
<br>
I have a quick question regarding which Gromacs force field in pdb2gmx is best suited for creating a topology (itp) file for the enzyme, lactate oxidase. So far the force fields in Gromacs 4.0.4 are:<br>
<br>
0: GROMOS96 43a1 force field<br>
1: GROMOS96 43a2 force field (improved alkane dihedrals)<br>
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
6: [DEPRECATED] Gromacs force field (see manual)<br>
7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>
8: Encad all-atom force field, using scaled-down vacuum charges<br>
9: Encad all-atom force field, using full solvent charges <br>
I selected the "G53a6 GROMOS96 53a6 Forcefield" for creating my itp file, however, when I try to run grompp to generate the .tpr file, I get the error:<br>
<br>
-------------------------------------------------------<br>
Program grompp_d, VERSION 4.0.4<br>
Source code file: toppush.c, line: 947<br>
<br>
Fatal error:<br>
Atomtype Qd not found<br>
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<br>
I've looked into other discussions on this (<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg15722.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg15722.html</a>), and concluded that the atomtype Qd must not be present in the G53a6 force field. My system is simply the protein lactate oxidase. Does anyone have suggestions on which force field(s) is best suited for this molecule?<br>
<br>
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Since the atom type "Qd" is not present in the 53a6 parameter set, this error has nothing to do with the appropriateness of your force field choice. Somewhere, you've incorporated a nonsensical atom type. The only time I have ever seen "Qd" is in the MARTINI coarse grain force fields. Be sure you're using the topologies you think you are; if you really are using an unaltered pdb2gmx-generated topology for 53a6, there is no way that this atom type would be found therein.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks in advance,<br>
Lili<br>
<br>
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-- <br>
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<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">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>
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