I want!!!<br><br><div class="gmail_quote">On Thu, Aug 6, 2009 at 6:48 AM, David Mobley <span dir="ltr"><<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I've got a toolkit I'm getting ready to release that does a whole bunch of things; the one that pertains to this discussion is that it uses MCCE to assign protonation states and add protons. The proton positions and protonation states are optimized based on environment if I understand correctly. It's possible it might solve your problem. Unfortunately at this point it's specific for the AMBER force field, though that's just an issue of residue/atom naming.<br>
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I can give you access to it if you're interested in checking it out. The reason it is not released yet is just that there's still various cleaning up that I need to do, and I need to add some licensing (GPL), etc.<br>
<br>
David Mobley, Ph.D.<br>
Assistant Professor of Chemistry<br>
University of New Orleans<br>
New Orleans, LA 70148<br>
<a href="mailto:dlmobley@uno.edu" target="_blank">dlmobley@uno.edu</a><br>
Phone 504-383-3662<br>
Fax 504-280-6860<div><div></div><div class="h5"><br>
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On Aug 6, 2009, at 8:40 AM, Michel Cuendet wrote:<br>
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Dear all,<br>
<br>
I am currently simulating a peptide bound to a protein. The peptide would very quickly deviate from the crystal structure. It turned out that this was due to the fact that an H-bond to a tyrosine sidechain could not be formed, because of the way the hydrogen was constructed on OH. Despite 300ps of equilibration with restraints on heavy atoms, this hydrogen was not able to rotate and find its natural H-bonding partner. As soon as restraints were removed, the peptide would adopt a wrong conformation. Building hydrogens elsewhere before starting the simulation solved the problem.<br>
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This sort of issue with potentially severe consequences on the outcome of a simulation could be avoided with an (even very crude) step of optimization when the free to rotate hydrogens of Tyr, Thr or Cys are constructed.<br>
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Charmm has a simple protocol:<br>
<a href="http://www.charmm.org/documentation/c35b1/hbuild.html" target="_blank">http://www.charmm.org/documentation/c35b1/hbuild.html</a><br>
<br>
And there are more sophisticated tools from which to get some inspiration:<br>
Reduce : <a href="http://kinemage.biochem.duke.edu/software/reduce.php" target="_blank">http://kinemage.biochem.duke.edu/software/reduce.php</a><br>
PDB2PQR : <a href="http://pdb2pqr.sourceforge.net/" target="_blank">http://pdb2pqr.sourceforge.net/</a><br>
<br>
OK, this was the suggestion, now who will implement it ... :0)<br>
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Should this be added to the oldwiki or somewhere?<br>
<br>
Best,<br>
Michel<br>
<br>
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-- <br>
<br>
==========================================================<br>
Michel Cuendet, Ph.D<br>
Molecular Modelling Group<br>
Swiss Institute of Bioinformatics<br>
CH-1015 Lausanne, Switzerland<br>
<a href="http://lausanne.isb-sib.ch/~mcuendet" target="_blank">http://lausanne.isb-sib.ch/~mcuendet</a><br>
==========================================================<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>