Dear all
I'm studying an enzymatic reaction using semi-empirical QM/MM Metadynamics.
I'm using amber12 as MD engine and Plumed to enable metadynamics.
Unfortunately I have a very big problem.
In practice I'm investigating a deprotonation of a serine residue by
an hystidine; at the beginning of the simulation the geometry of the
system is well described, however after the deprotonation happens the
serine residue takes the hydrogen atom bound to one of the carbon
atoms of the hystidine ring.
I've tried different semiempirical methods as DFTB with 3rd order
correction, or PM6, PM6-DH+ but I still have this problem.
In the initial phase of my study I had a negatively charged QM part
and maybe I could have problems related with electron delocalizations,
then I have reduced the QM part and now I have only serine and
hystidine (the minimal system to investigate the reaction).
Did anybody have the same experience? Do you have advices?
Thanks a lot
Jacopo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 21 2012 - 07:30:04 PST
