Hi Andrea,
You're probably best off 'fixing' the copper to the protein, meaning
introducing bonds at least (harmonic, type 6?). With these bonds you
can to some degree account for the effects of polarization and such on
the interatomic distances, which are likely more difficult to model
reparameterizing the non-bonded interactions. You should also
definitely consider that there is considerable polarization and charge
transfer in such metal clusters, which means that you should probably
attenuate the charges of the copper as well as of the ligating atoms.
For the ligation geometry you can try to rely on size-exclusion
effects of the ligands, but copper may prove nasty, in which case you
also need to set parameters for angles and maybe for dihedrals. Not
for naught that newbies are usually discouraged for performing
simulations like these (exotic species)... But you had already
considered that.
Hope this helps,
Tsjerk
On Wed, Aug 12, 2009 at 12:40 PM, andrea
spitaleri<spitaleri.and...@hsr.it> 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
>
> --
> -------------------------------
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> Tel: 0039-0226434348/5622/3497/4922
> Fax: 0039-0226434153
> http://sites.google.com/site/andreaspitaleri/
> -------------------------------
>
> -----------------------------------------------------------------
>
> La tua mano puo' lasciare un segno importante.
> Dona il tuo 5 per mille al San Raffaele di Milano.
>
> E' SEMPLICE E NON COSTA NULLA.
> Basta indicare nell'apposito riquadro della dichiarazione dei redditi
> "Finanziamento della ricerca sanitaria"
> il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
> 03 06 42 80 153 e ricordarsi di firmare.
> Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org.
> _______________________________________________
> gmx-users mailing list gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
