[gmx-developers] Suggestion : hydrogen generation
ichorny at gmail.com
Thu Aug 6 16:22:06 CEST 2009
On Thu, Aug 6, 2009 at 6:48 AM, David Mobley <dmobley at gmail.com> wrote:
> 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.
> 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.
> David Mobley, Ph.D.
> Assistant Professor of Chemistry
> University of New Orleans
> New Orleans, LA 70148
> dlmobley at uno.edu
> Phone 504-383-3662
> Fax 504-280-6860
> On Aug 6, 2009, at 8:40 AM, Michel Cuendet wrote:
>> Dear all,
>> 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.
>> 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.
>> Charmm has a simple protocol:
>> And there are more sophisticated tools from which to get some inspiration:
>> Reduce : http://kinemage.biochem.duke.edu/software/reduce.php
>> PDB2PQR : http://pdb2pqr.sourceforge.net/
>> OK, this was the suggestion, now who will implement it ... :0)
>> Should this be added to the oldwiki or somewhere?
>> Michel Cuendet, Ph.D
>> Molecular Modelling Group
>> Swiss Institute of Bioinformatics
>> CH-1015 Lausanne, Switzerland
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Ilya Chorny Ph.D.
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