[gmx-users] Problems with HExxH-Zn coodrination in OPLSA ff

Jorge Hernandez Fernandez jorgehf at cbi.cnptia.embrapa.br
Sat Jan 7 20:11:32 CET 2006

Dear Gmx-ers (particularly Maik!): 

   We are working with Protein-ligand complexes, in metalloproteases. The Zn 
ion is pentacoordinated by 2 His, 2 Glu and external water (or ligand oxo 
group in the case of complex…). 
    All these distances/bonds were reasonably in our old gmxff <all-bond> 
dynamics (in 1.5 ns runs), but in new experiments (OPLSAA or Gromos ff), one 
(protonated) His is flying away from the coordinate position in 30-100 ps and 
Glu coordination become distorced. We would like some help to restrain all 
these residues and fix a more-less real charges for this group&#8230;&#8230; 
    As posted by Maik Goette 1-2 months ago in the list, is a python script 
that help fix all these positions. As we are in serious troubles trying to 
validate our old results in new long runs (in better ff), may you please share 
this scrip with us? 
       Any other clues to restrain the HEXXH-Zn group, bond distances and 
charges are welcome. Thanks all in advance: 

                                           Jorge H.F. 


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