Re: [AMBER] Reg:MMPB(GB)SA Error

From: David A Case <>
Date: Mon, 13 Apr 2020 15:16:12 -0400

On Mon, Apr 13, 2020, Lara rajam wrote:

>I am interested in calculating MMGBSA , when I tried for the complex (
>protein ligand complex)
>I got a value of
>DELTA TOTAL -5917.4803 1224.2734
>Can anyone tell me what could be wrong? , I checked prmtop all seems good.

Please look at recent posts on this list from Nada Afiva, which contain
some good suggestions for debugging.

Also, read carefully the beginning paragraphs of the chapter.
(The part about this not being a "black box").

Generally: run a *short* calculation (even just a few frames) using the
single trajectory approach. You will need three simulations: one for
complex, one for receptor and one for the ligand. Do the Delta
subractions yourself (not using the python script). Make sure that the
bond, angle and dihedral contributions to delta are zero. Visualize
each of the three systems, and look for any odd behavior you can find.

If you are off by 6,000 kcal/mol, it is likely that some of the
assumptions made by the python script don't apply in your case, or you
have some very odd energies. Breaking things down into individual
components may help, but debugging this sort of calculation (actually,
almost any free energy calculation) can require some detailed detective

...good luck....dac

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Received on Mon Apr 13 2020 - 12:30:02 PDT
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