Hi
Try using use_sander = 1 in your control file.
On Thu, 21 Jan 2021 at 12:50, Sadaf Rani <sadafrani6.gmail.com> wrote:
> Dear Amber user
>
> I am doing MMPBSA calculations on a 20ns trajectory for protein and ligand
> complex. I am getting error of cpptraj failed with ligand prmtop as
> mentioned below:-
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp complex.prmtop
> -cp complexdry.prmtop -rp protein_cofactordry.prmtop -lp G6P_n.prmtop -y
> Prod.crd
> Loading and checking parameter files for compatibility...
>
> /home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py:603:
> UserWarning: receptor_mask overwritten with default
>
> warnings.warn('receptor_mask overwritten with default\n')
> cpptraj found! Using /home/rcms/Downloads/Amber/amber20/bin/cpptraj
> mmpbsa_py_energy found! Using
> /home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
> Preparing trajectories for simulation...
> 2000 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> File "/home/rcms/Downloads/Amber/amber20/bin/MMPBSA.py", line 100, in
> <module>
> app.run_mmpbsa()
> File
>
> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
>
> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
>
> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 475, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /home/rcms/Downloads/Amber/amber20/bin/cpptraj failed with
> prmtop G6P_n.prmtop!
>
> I am new in doing this calculation, could anyone please help me to figure
> out the problem why I am getting this error and how should I fix it. Any
> suggestion would really be appreciated.
> Thanks in advance.
> Regards
> Sadaf
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>
--
Best Regards
Elvis
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Received on Thu Jan 21 2021 - 00:00:02 PST
