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/
-------------------------------
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