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 - 09:30:02 PDT
