Dear Amber community,
I have an NAD dehydrogenase system
NAD + A <-> NADH + B
with XRC coordinates for
1) NAD-protein complex and
2) abortive ternary complex NAD-B-protein
The abortive ternary complex structure is significantly different
than the NAD-protein complex, and is a dead-end, non-productive structure.
I want to model in explicit water the more physiologic NAD-A-protein
complex, which is simply accomplished by changing the the C=O group of
B to a hydroxy group of A.
Since I have no idea if the productive complex is significantly different
than the abortive complex, I want to shake things up a bit.
After normal restrained simulations to equilibrate water, etc, etc, I was
planning on a 400 C simulation without restraints for 1 ns and then
a 1 ns simulation from 400 to 300 C with gamma_ln=0.02 for a slow cool, and
then typical langevin temperature control for production md.
Is this reasonable? Any suggestions or comments would be welcome!
Thanks so much in advance.
Dean
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Received on Tue May 04 2010 - 13:30:03 PDT
