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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

Date: Thu, 10 Jul 2014 11:11:17 -0700

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

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jul 10 2014 - 11:30:03 PDT

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