<br><br><div><span class="gmail_quote">On 1/9/06, <b class="gmail_sendername">Joanne Hanna</b> <<a href="mailto:J.F.Hanna@warwick.ac.uk">J.F.Hanna@warwick.ac.uk</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br><br>Yes that might be the source of my problem I have not checked this.<br>Thanks for the suggestion.<br>When you use autodock do you use the kollman charges and gasteiger<br>charges for ligands?</blockquote><div><br>
Yes, I do. MG </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Thanks<br>Jo<br><br>Joanne Hanna<br>Department of Chemistry<br>University of Warwick
<br>Coventry<br>CV4 7AL<br><br><a href="mailto:J.F.Hanna@warwick.ac.uk">J.F.Hanna@warwick.ac.uk</a><br>>>> <a href="mailto:magiofer@gmail.com">magiofer@gmail.com</a> 01/09/06 10:26 AM >>><br>Hi Jo,<br>well, I used to employ both GROMACS and AutoDock on my systems, but
<br>usually<br>the only format incompatibility I can think of is about residue naming,<br>for<br>instance I used HISA and HISB, LYSH and CYSH protonation, they should be<br>renamed (without changing protonation of course) to HIS, LYS and CYS.
<br>Besides, if you have aromatic carbons in your ligand, you should change<br>their atom types from C to A, using the AutoDock function in the Ligand<br>menu.<br>That's all I think.<br>I hope it helps.<br>MG<br><br>On 1/9/06, David van der Spoel <
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>><br>> Joanne Hanna wrote:<br>> > Hi<br>> ><br>> > I was wondering whether anyone on the list has experience using<br>gromacs
<br>> > output (with polar Hs) in autodock, as I am struggling with some<br>kind of<br>> > seemingly random file format incompatibility.<br>> > I was also wondering whether when using autodock people use the
<br>kollman<br>> > charges or the gmx ff charges for their macromolecule and for<br>ligands<br>> > the charges they have derived for their own topologies or the<br>gasteiger<br>> > charges.<br>> > I thought it was possibly best to be self consistent and use the
<br>same<br>> > charges that I have used for docking as I have and will in MD<br>> > simulations.<br>> ><br>> > Sorry its a bit of a waffley question.<br>><br>> You should probably use charges that Autodock usually uses, since it
<br>> also has its own LJ parameters.<br>><br>><br>> ><br>> > Hope someone can help<br>> ><br>> > Jo<br>> > _______________________________________________<br>> > gmx-users mailing list
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<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755
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