Dear Andrea,
Which restraints did you use?
I've ran simulations on a similar system (Zn2+ coordinated to
histidines) with NMR restraints as implemented in Gromacs and it worked
fine.
Best regards,
Ran.
andrea spitaleri wrote:
> Dear all,
> I am going to run some MD simulation of a protein bearing a copper cluster (3
> Cu2+ nominally charge
> 2+) coordinates to histidine residues. As far as concerning the importance of
> this cluster in the
> enzymatic activity (this would require QM/MM), my issue is how to interpret
> the "whole" system
> [HIS_{2}-Cu2+]_{3} in term of force field. From literature and from previous
> posts in this mailing
> list, in MD system similar to mine (aminoacid coordinating ions) are treated
> as an unique "residues"
> (i.e. HEME group). My first try was to perform MD without restraints on Cu2+,
> but unfortunately at
> 100K (I am doing an equilibration from 100K to 300K) after few ps one of the
> Cu2+ left already its
> position (basically it is flying away).
> Second try was to put restraints on the system between the Cu2+ and the
> N-HIS. However, my doubt is
> how bad is this assumption respect to the possibility to consider the whole
> system Cu2+-HIS as an
> unique residue in the topology file. I am aware that for the latest
> hypothesis I should reconsider
> all the properties (i.e. charges, angles, etc ...), so a long way and hard
> work. Think about that I
> need to put a O2 molecule inside of the Cu2+ cluster in a second study.
>
> Any suggestion, comments and anything else are very welcome.
>
> Thanks in advance
>
> Regards
>
> andrea
>
>
--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
------------------------------------------------------
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