Dear Amber Users,
I have run several tests for P450 (human and from Pseudomonas Putida)
using force field for heme provided by Rydberg et al.
General Transition-State Force Field for Cytochrome P450 Hydroxylation
Patrik Rydberg, Lars Olsen, Per-Ola Norrby, Ulf Ryde,
Journal of Chemical Theory and Computation 2007 3 (5), 1765-1773.
Since the beginning of the simulation I observe elongation of the distance
between iron (heme) and sulfur (CYS, axial ligand of heme) from 2.34 A in
the X-ray structure to 3.25 A average over 2ns production run. This
elongation is systematic, just in one case the distance was longer – 5.1 A
averaged over 2 ns production run.
Value given by Rydberg et al. for Fe-S is 2.3253 A, and force constant
296.436 kcal/mol-1 A-2. But they do not discuss this distance neither for
a training set nor for a test set.
Other distances and angles look reasonable and are in agreement with the
literature data.
I have not yet tried other force field for heme.
My question is if someone had similar experience with this force field?
Maybe someone can give me hints where to look for the source of this
artificial elongation of the Fe-S distance?
Thanks,
Renata
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Received on Tue Jun 08 2010 - 08:00:06 PDT
