Dear Amber users,
I've been simulating a reaction with QM/MM method. In my catalytic
reaction center I have i salt bridge exposed to the media and that close
it. During 20 ns, that bridge is stable, but when I introduce it QM
calculation it starts to be unstable. Revising the structure, I see it
interacts with solvent water. These waters are a TIP3 box and I have one
question: could it be a problem between TIP3 and QM region because their
high diffusion coefficient, and so, it could try to broke my bridge
(between an arginine and glutamic)? What kind of water would be better
to use?.
Thank you,
--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 5.
UAM University. Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
Web: http://fertoledo.wordpress.com/
==============================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 20 2012 - 01:30:04 PDT
