Update:
I've checked additionally temporary pdb filles produced during the
calculations and found that the lipid atoms are still present in all
three pdbs (complex, receptor, ligand) althoug I indicated to strip
them during the processing : ':WAT:Cl-:Na+:K+:OL:PC:PA'
would it be possible alternatively to define another strip mask to
strip everything but not protein atoms ?
Il giorno mer 6 set 2023 alle ore 18:03 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> 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 Wed Sep 06 2023 - 09:30:03 PDT
