transition metal parameters

From: Francesca Lønstad Bleken (
Date: Fri Jun 24 2016 - 02:19:01 CDT


I wish to do MD on a Cu containing Enzyme with NAMD and have a question on
the treatment of the Cu and amino acids bound to the Cu as well as
force field choice. Similar systems to ours have been used before and they have used
GROMOS96 and OPLS2005 and kept bonds and angles to the
Cu atoms fixated. I intend to do similarly, but am thinking about using CHARMM36 if possible.
As far as I can see there are no CHARMM parameter for Cu(I) or (II).
Are these available and usable with NAMD? If not, what forcefield do you suggest to use or have experience with on similar problems?
I am also not entirely sure how to treat the amino acids
connected to the Cu..

I am aware that I will not be able to study chemistry of the part of the enzyme close to the Cu with this method
(we do QM for that). With this I wish to look at the stability of the various parts of the enzyme (not close to Cu as these are fixed)
over time.

I am grateful for any help/directions/links/tutorials.

Best regards,

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:34 CST