Re: [AMBER] FINAL RESULT MMPBSA QUERY

From: Ray Luo <rluo.uci.edu>
Date: Wed, 18 Nov 2020 21:47:25 -0800

Manisha,

Looks like you are running the tutorials with Amber 14?

One possible reason is that different options might be used to set PB
radii between the two runs. You can set radiopt=0 in the pb section of
the input to make sure the radii in prmtop files are always used.

Also, your PB run was set to compute nonpolar solvation energies for
INP=2. You can set INP=1 in the pb section of the input to use the
classical approach to compute nonpolar solvation energies, which is
how many MMPBSA runs were done in the literature.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Tue, Nov 17, 2020 at 11:59 PM Manisha <manishachauhan0403.gmail.com> wrote:
>
> Hello,
> I tried doing the tutorial given on the AMBER site for both GBSA AND PBSA.
> The input file that I have attached below is the FINAL RESULT file and if I
> were to compare both the files ( given on site and mine) , the gbsa values
> are similar but there is drastic change in the pbsa total values.
> please help me solve this problem as I shall be running my own protein DNA
> complex for binding energy afterwards.
>
> Thank you
>
> Sincerely,
>
> *Manisha*
>
> *Ph.D. Scholar*
>
> Multidisciplinary Centre For Advanced Research and Studies
>
> Jamia Millia Islamia
>
> Delhi-110025
>
> Ph.no: 9518014737
>
>
> [image: Image result for save world by plant][image: Image result for save
> world by plant white background]
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Received on Wed Nov 18 2020 - 22:00:02 PST
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