Thanks a lot Jason.
On Thu, Jul 10, 2014 at 11:41 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> 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 - 21:00:02 PDT
