Hello Debarati,
In my opinion anions should be removed from ligand and receptor file and you
may expect completed results from MMBPSA.py calculation.
Cheers,
Zoran
-----Original Message-----
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Sunday, November 14, 2021 12:21 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MMGBSA error mitigation
I used ante-mmpbsa.py 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]$ ante-MMPBSA.py -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''
b'Traceback (most recent call last):\n File
"/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-ext
ernal/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-ext
ernal/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/metadata.py",
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/metadata.py",
line 177, in from_name\n raise
PackageNotFoundError(name)\nimportlib.metadata.PackageNotFoundError: ParmEd'
From: Debarati DasGupta<mailto:debarati_dasgupta.hotmail.com>
Sent: 13 November 2021 17:54
To: AMBER Mailing List<mailto:amber.ambermd.org>
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?
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 - 16:00:02 PST
