After pdb2gmx of the whole structure, make an index file and them run another pdb2gmx choosing the c-alpha group. I hope it helps.<br><br><div><span class="gmail_quote">2008/6/20, Lillian Chong <<a href="mailto:ltchong42@gmail.com">ltchong42@gmail.com</a>>:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users,<br> <br> I would like to generate a topology for a protein in which each<br> residue is represented only by its C-alpha atom (a Go-type model).<br> What would be the most straightforward way of creating this topology<br>
file?<br> <br> Thanks in advance,<br> Lillian<br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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