# Re: [AMBER] entropy Calculation

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 10 Jul 2014 11:11:17 -0700

On Jul 10, 2014, at 9:30 AM, Him Shweta <shwetahim.gmail.com> wrote:

> Hi, Jason
>
> Here i am attaching the MMPBSA_complex_nm.out, MMPBSA_receptor_nm.out,
> MMPBSA_ligand_nm.out, Final output file of the entropy calculation with
> drms=0.1,
> Can you please explain me the nm.out files. As you said that negative
> eigenvalues are omitted from entropy calculation.

​Go down to where it says "- Thermochemistry -". The modes are enumerated in order of increasing eigenvalue (which is decreasing vibrational entropy).

- Thermochemistry -

Temperature: 298.150
Pressure: 1.000
Mass: 7224.836
Principal moments of inertia in amu-A**2:
430593.53 494797.92 572258.97
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
found 1 imaginary frequencies
Zero-point vibrational energy: 3521.312

freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 2670.620 1683.246 2006.885
translational: 0.888 2.979 52.441
rotational: 0.888 2.979 50.653
vibrational: 3791.941 1677.288 1903.790
ff energy: -1123.097
1 -1.893
2 -0.000
3 0.000
4 0.000
5 0.544
6 0.736
7 0.809
8 2.075 0.592 1.986 11.127
9 3.988 0.592 1.986 9.830
10 4.790 0.592 1.986 9.466
11 5.122 0.592 1.986 9.333
12 5.522 0.592 1.986 9.183
...

There is one mode that is "significantly" negative (i.e., < -0.5 cm^-1). This is pegged as an imaginary frequency (and the next 6 modes are omitted as translational and rotational modes that are incorporated via standard formulae).

If you were actually at a minimum, that -1.893 cm^-1 eigenmode would not have had a negative eigenvalue. Your ligand had 3 imaginary frequencies and your receptor had 1 imaginary frequency. And you can see how much low-frequency modes contribute to the total entropy. So I suspect that these frequencies change enough to result in large changes in the total entropy when you get closer to a true minimum.

Hope this helps,
Jason

```--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 10 2014 - 11:30:03 PDT
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