Hello there!
Do you mean the single quotes for the ligand mask -n :240-250 corresponded
to 10 amino acids? Actually, beforehand dealing with an organic ligand
residue, I had used it as -n :lig and it worked fine without quotes..
Also I have not noticed any issue on the step of the creation of stripped
parmtop since everything looks fine and there is no lipids in any of these
filles ( checked every parmtop ..)
The problem arises at the very first step of the computing dG using these
filles with mmgbsa.py script that produces temporary pdb and netcdf with
lipids ( which should be normally stripped ).
Finally I forgot to mention that I am dealing with membrane protein system
created according to the tutorial using lipids21 which devided each lipid
onto two residues (indicated in stripped mask along with :wat, ions etc ).
I am going to perform extensive benchmark tests and will report my progress.
Yours with thanks
Enrico Martinez
Le mer. 6 sept. 2023 à 19:10, Ramachandran, Balajee <rbalajee.bu.edu> a
écrit :
> I guess the error issue raised because of the quotes. The numbering
> should be in single quotes for ante-MMPBSA. Otherwise, check the structure
> ------------------------------
> *From:* Enrico Martinez via AMBER <amber.ambermd.org>
> *Sent:* Wednesday, September 6, 2023 12:03 PM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] Issue with MMPBSA calculation
>
> Dear Amber Users
>
> I faced the issue during MMBSA calculations for protein-peptide
> complex. In my system the ligand corresponded to the fragment of 10
> aminoacids (:240-250)
>
> First I successfully make a stripped trajectories using
>
> ante-MMPBSA.py -p ${prmtop} -c complex.prmtop -r receptor.prmtop -l
> ligand.prmtop -s ':WAT:Cl-:Na+:K+:OL:PC:PA' -n :240-250
>
> that produced 3 prmtop files for complex, ligand and receptor which I
> checked in VMD and it looks OK
>
> Then I run
>
> MMPBSA.py -O -i mmgbsa.in -o mmgbsa.dat -do DECOMP.dat -sp ${prmtop}
> -cp complex.prmtop -rp receptor.prmtop -y *.nc -lp ligand.prmtop
>
> 29 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /opt/site/ubuntu_22.04/amber/22b/bin/sander
> calculating complex contribution...
>
>
> and here is the error:
>
> File "/opt/site/ubuntu_22.04/amber/22b/bin/MMPBSA.py", line 100, in
> <module>
> app.run_mmpbsa()
> File
> "/opt/site/ubuntu_22.04/amber/22b/lib/python3.10/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/opt/site/ubuntu_22.04/amber/22b/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/opt/site/ubuntu_22.04/amber/22b/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> line 156, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /opt/site/ubuntu_22.04/amber/22b/bin/sander failed with
> prmtop complex.prmtop!
>
> I've checked complex.parmtop produced by ante-mmbsa and did not find
> any errors with it. Could you suggest what could be fixed with it ?
>
> Yours with thanks
>
> Enrico
>
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Received on Thu Sep 07 2023 - 01:00:02 PDT
