[gmx-developers] Suggestion : hydrogen generation

Michel Cuendet michel.cuendet at isb-sib.ch
Thu Aug 6 15:40:18 CEST 2009

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 

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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