Dear Amber Users,
I am performing a SMD simulation for an enzyme reaction with three steps
happening in a concerted manner. Though I was able to achieve the three
steps but the energy barrier for all the three steps is around 60 kcal/mol.
What could be the reason for such a high energy? I was suggested previously
to perform SMD for a single step first and lower the harm value. Since I am
following this paper where all the three steps were performed in a single
SMD simulation (
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004051),
I cannot perform SMD for invidual steps, as this will not solve my purpose.
So, I tried to lower the harm value and performed the simulation again,
then in this case, I was not able to see all three steps occurring
together.
I would highly appreciate if somebody could tell how can I get a reasonable
energy barrier for all the three steps?
--
*Best Regards*
Bharat
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Received on Thu Jul 21 2016 - 07:30:02 PDT
