Re: [AMBER] MMGBSA error mitigation

From: Debarati DasGupta <>
Date: Sat, 13 Nov 2021 22:53:36 +0000

Hello Prof Case
One small query regarding creation of prmtop files for MMGBSA type calculations
Should the dry_complex(non solvated) be neutralized with counterions to keep net charge 0 same for receptor prmtop and ligand?
My solvated complex prmtop is neutralized with 6 Cl- ions, I was wondering should I keep my receptor.prmtop and the non solvated complex.prmtop also neutralized otherwise the total atoms would not match.

Any idea?

From: David A Case<>
Sent: 13 November 2021 08:42
To: AMBER Mailing List<>
Subject: Re: [AMBER] MMGBSA error mitigation

On Sat, Nov 13, 2021, Debarati DasGupta wrote:
>I am trying to compute the binding affinity of a ligand to a mark4kinase.

>I see it says fatal error with the protein.prmtop I checked it 3 times it
>looks fine just the receptor and chloride ions are in the prmtop.

Ordinarily, one would strip both water and ions from these prmtop files.
You might try this.

>Fatal Error!
>All files have been retained for your error investigation:
>You should begin by examining the output files of the first failed calculation.
>Consult the "Temporary Files" subsection of the chapter in the
>manual for file naming conventions.

Did you look at the output files for more information about the error?
Also, running the calculation "by hand" might help: see the second paragraph
in Chapter 36 of the reference manual.

...good luck....dac

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