Dear Elvis
I added use_sander=1 in the input file as below:-
Input file for running PB and GB
&general
endframe=2000, verbose=1,receptor_mask=":1-491",
strip_mask=":Na+:WAT",use_sander=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
However, I am getting an error with the complex prmtop file now as
mentioned below:-
Beginning GB calculations with /home/rcms/Downloads/Amber/amber20/bin/sander
calculating complex 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 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/rcms/Downloads/Amber/amber20/bin/sander failed with prmtop
complexdry.prmtop!
Exiting. All files have been retained.
What else should I try to fix this error? Please guide me.
Thanks in advance.
Sadaf
On Thu, 21 Jan 2021 at 12:53, Elvis A F Martis <martiseaf.elvismartis.in>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best Regards
> Elvis
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 24 2021 - 21:00:02 PST
