Re: [AMBER] MMGBSA error mitigation

From: Debarati DasGupta <>
Date: Sat, 13 Nov 2021 23:21:05 +0000

I used on Amber20 manual page 758
Still I see this error my residue mask 1-307 is receptor residue 308 is my ligand...

[debarati.login02 mmpbsa]$ -p complex_solvated.prmtop -c complex_dry.prmtop -l ligand.prmtop -n :308 -r protein.prmtop
Creating receptor topology file by stripping :308 from complex_solvated.prmtop
Error: Creating receptor topology failed!
b'Traceback (most recent call last):\n File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/parmed", line 33, in <module>\n sys.exit(load_entry_point(\'ParmEd==3.4.1\', \'console_scripts\', \'parmed\')())\n File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/parmed", line 22, in importlib_load_entry_point\n for entry_point in distribution(dist_name).entry_points\n File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/python-3.8.5-naaw62bifnds2nzcxoazwqbb5bok4u4r/lib/python3.8/importlib/", line 504, in distribution\n return Distribution.from_name(distribution_name)\n File "/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/python-3.8.5-naaw62bifnds2nzcxoazwqbb5bok4u4r/lib/python3.8/importlib/", line 177, in from_name\n raise PackageNotFoundError(name)\nimportlib.metadata.PackageNotFoundError: ParmEd'

From: Debarati DasGupta<>
Sent: 13 November 2021 17:54
To: AMBER Mailing List<>
Subject: Re: [AMBER] MMGBSA error mitigation

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

AMBER mailing list

AMBER mailing list

AMBER mailing list
Received on Sat Nov 13 2021 - 15:30:02 PST
Custom Search