Dear Amber Users
I need help in diagnosing an error with MMGBSA.
When I try to run an MMGBSA analysis on a trajectory (the trajectory looks
absolutely fine on VMD and inspection in a text editor also shows no
issues), I get the following error:
MMPBSA.py -O -i mmgbsa1.in -sp wt_wat.top -cp complex.top -rp rec.top -lp
lig.top -y imaged1.crd -o mmgbsa1.dat -do decomp1.dat > mmgbsa1.out &
[1] 23047
(ambertools-20220513) [sugupta.n099 water-md]$ File
"/packages/miniconda/20190102/envs/ambertools-20220513/bin/MMPBSA.py", line
100, in <module>
app.run_mmpbsa()
File
"/packages/miniconda/20190102/envs/ambertools-20220513/lib/python3.10/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/packages/miniconda/20190102/envs/ambertools-20220513/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/packages/miniconda/20190102/envs/ambertools-20220513/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
line 156, in run
raise CalcError('%s failed with prmtop %s!' %
(self.program,
CalcError:
/packages/miniconda/20190102/envs/ambertools-20220513/bin/sander failed
with prmtop complex.top!
Fatal Error!
All files have been retained for your error
investigation:
You should begin by examining the output files of the
first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in
the
manual
for file naming conventions.
[1]+ Exit 1
MMPBSA.py -O -i mmgbsa1.in -sp wt_wat.top -cp complex.top -rp rec.top -lp
lig.top -y imaged1.crd -o mmgbsa1.dat -do decomp1.dat > mmgbsa1.out
(ambertools-20220513) [sugupta.n099
water-md]$
The mmgbsa input that I am using is:
MMPBSA.py input file for running GB
&general
startframe=1,
endframe=500, interval=100,
keep_files=0, netcdf=1,
/
&gb
igb=5, saltcon=0.1
/
&decomp
idecomp=4, dec_verbose=0, csv_format=0
Please help me solve this.
Have never ever faced this issue earlier and the system is a very simple
one with HIV-1 Protease and a natural substrate (so no forcefield issues
too)
Thanks
Suchetana
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Received on Wed Feb 01 2023 - 15:00:02 PST
