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?
Thanks
Debarati
From: David A Case<mailto:david.case.rutgers.edu>
Sent: 13 November 2021 08:42
To: AMBER Mailing List<mailto:amber.ambermd.org>
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 MMPBSA.py 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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Received on Sat Nov 13 2021 - 15:00:02 PST
