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

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Jan 9 16:42:32 CET 2006

Dear Jorge

I am sorry, that my script propably won't help you.
It searches for sulphurs in CYSs. Thats the first problem.
It further attaches bonds and angles to the topology file, which 
restrict the zinc ion from diffusing away. This is only practicable, if 
the zinc isn't included in binding, I suppose.
The charges, it attaches to the zinc, depend on data for a 4-coordinated 
zinc ion.Thats the second problem.
If you are able to modify python-"code" to search for the glutamate and 
the water oxygen and some other things, it should work.
The scientifc-package has to be installed also.
If you still want it, send me a mail and I will send it to you.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Jorge Hernandez Fernandez wrote:
> 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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