[gmx-developers] Suggestion : hydrogen generation

David Mobley dmobley at gmail.com
Thu Aug 6 15:48:28 CEST 2009

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),  

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:
> http://www.charmm.org/documentation/c35b1/hbuild.html
> 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?
> Best,
> Michel
> -- 
> ==========================================================
> Michel Cuendet, Ph.D
> Molecular Modelling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne, Switzerland
> http://lausanne.isb-sib.ch/~mcuendet
> ==========================================================
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list