AMBER Archive (2006)

Subject: Re: AMBER:

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 21 2006 - 00:36:09 CST

On Mon, Mar 20, 2006, emilia wu wrote:
>
> i came cross a problem which confuse me for several days. i am studing the
> bingding of a protein and ligand with MMPBSA.
> but i found something is wrong with my result of entropy. i copy a part of my output file here.
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> TSTRA -13.50 0.00
> TSROT -11.38 0.02
> TSVIB 1.83 8.95
> TSTOT -23.05 8.97
>
> i am wondering why the value of TSVIB is positive, and what this means? i
> think it should be negative just from the
> physical intuition. is it means my parameters of ligand is not accurate?

Your "physical intuition" is probably wrong. There is no reason for the change
in vibrational entropy to be one sign or the other -- we have seen both
results in our work. The variance from one point to another seems pretty
high, but of course I have virtually no idea what sort of calculation you are
doing.

...dac

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