Hi Tsjerk,
thanks for the usual useful suggestions! Probably I will go for that, add an
harmonic bonds between
Cu2+ and N-HIS and I will think how to hand the charges too.
Probably this is the less worst solution for now.
Thank a lot,
Regards
andrea
Tsjerk Wassenaar wrote:
> 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-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
>>
>
>
>
--
-------------------------------
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-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
