Dear Amber Users Community:
As far as I know, NMA calculates the vibrational frequency for each normal
mode. And these frequencies are used to calculate configurational entropy
(I call it as Svib) in NAB program if nmode() is called. An entropy term
will then be reported. And then in terms of application in my case which is
binding energy calculation, I put delta enthalpy calculated from MM/PBSA
and delta entropy calculated from NMA to obtain a delta G.
As I am reviewing NMA basics, I noticed that in theory, low frequency
vibration (lower than 500 cm-1) could have non-negligible contribution to
enthalpy. Cases include torsional vibration, ring bending vibration, etc.
Therefore, I am wondering if the nmode() in NAB also calculate this part of
contribution to enthalpy (I call it as Hvib)? If yes, which part of output
indicate that? If not, is it possible to include Hvib from somewhere else?
Another question is then related to my application in binding energy
calculation. The MM/PBSA method has already constructed a thermal dynamic
cycle to give an energy difference before and after binding event. Svib is
added to cancel out its over-estimation to ideally give a more realistic dG
value that is close to experimental data. From this perspective, is Hvib
already considered in MM/PBSA internally in a more force-field or empirical
way, although it is not explicitly listed out as a single term?
Thank you for your time! If meantime, you think there are some good
reference or materials that could clarify my confusions, I really
appreciate that if you could share with me!
Best,
Guqin
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
https://www.linkedin.com/in/guqin-shi-029bb634
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Received on Thu Apr 20 2017 - 16:00:03 PDT
