Dear Amber Developers,
I am trying running nmode calculation for protein-ligand complex
(Cytochrome system) for initial 1 or 2 frames for entropy calculation with
the following input file and command:
Input file for running GB and mode
&general
startframe=20, endframe=1000, interval=50,
keep_files=2
/
&gb
igb=2, saltcon=0.100,
/
&nmode
maxcyc=100, nmendframe=1,
nmode_igb=1, nmode_istrng=0.1,
/
command:
/home/software/ambergnu/amber22/bin/MMPBSA.py -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp complex_solv_md.prmtop -cp
complex_dry_md.prmtop -rp receptor_dry.prmtop -lp ligand.prmtop -y
final.1.nc > progress.log
-------------------------------------------------------------------------------------------------------------------------
This calculation gives an error (pasted below) that i am unable to
understand and find any solution for it. Please provide possible solution
for this error or any other suggestions are also helpful.
Line minimizer aborted: step at upper bound 0.0024676232
Line minimizer aborted: step at upper bound 0.012140098
Line minimizer aborted: step at upper bound 0.03788681
Line minimizer aborted: step at upper bound 0.0012700911
Line minimizer aborted: step at upper bound 0.0093337326
Line minimizer aborted: step at upper bound 0.046959281
Line minimizer aborted: step at upper bound 0.00019163286
Line minimizer aborted: step at upper bound 0.079604343
Line minimizer aborted: step at upper bound 0.00044661187
Line minimizer aborted: step at upper bound 0.0011045502
Line minimizer aborted: step at upper bound 0.082978387
Line minimizer aborted: step at upper bound 0.042741479
Line minimizer aborted: step at upper bound 0.0033774559
Line minimizer aborted: step at upper bound 0.0049827848
Line minimizer aborted: step at upper bound 0.0044372613
Line minimizer aborted: step at upper bound 0.064660703
Line minimizer aborted: step at upper bound 0.00028338204
Line minimizer aborted: step at upper bound 0.00069139542
Line minimizer aborted: step at upper bound 0.0016381337
Line minimizer aborted: step at upper bound 0.00035699373
Line minimizer aborted: step at upper bound 0.053375613
Line minimizer aborted: step at upper bound 0.0020937967
Line minimizer aborted: step at upper bound 0.0031216561
Line minimizer aborted: step at upper bound 0.0037521567
Line minimizer aborted: step at upper bound 0.00013973399
Line minimizer aborted: step at upper bound 0.049772459
Line minimizer aborted: step at upper bound 0.0077299037
Line minimizer aborted: step at upper bound 0.00019173903
Line minimizer aborted: step at upper bound 0.018564367
Line minimizer aborted: step at upper bound 4.9858388e-05
Line minimizer aborted: step at upper bound 0.0067258898
Line minimizer aborted: step at upper bound 0.06992304
Line minimizer aborted: step at upper bound 0.029330483
Line minimizer aborted: step at upper bound 0.039871274
Line minimizer aborted: step at upper bound 0.0046801064
Line minimizer aborted: step at upper bound 0.0001613582
Line minimizer aborted: step at upper bound 0.00039150803
Line minimizer aborted: step at upper bound 0.0058031536
Line minimizer aborted: step at upper bound 0.001378761
Line minimizer aborted: step at upper bound 0.052916809
Line minimizer aborted: step at upper bound 0.0015673648
Line minimizer aborted: step at upper bound 0.0019233534
File "/home/vadlab/Amber22/bin/MMPBSA.py", line 108, in <module>
app.parse_output_files()
File
"/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py",
line 940, in parse_output_files
self.calc_types[key]['delta'] = BindClass(
File
"/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/amber_outputs.py",
line 1007, in __init__
self.delta2()
File
"/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/amber_outputs.py",
line 1239, in delta2
self.data[key] = [self.com.data[key].avg() - self.rec.data[key].avg() -
File
"/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/amber_outputs.py",
line 187, in avg
return (sum(self) / len(self))
ZeroDivisionError: division by zero
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.
Thank you for your anticipation!
Ankita Nishad
Dept. of Med Chem
NIPER Guwahati
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Received on Fri Mar 31 2023 - 04:00:02 PDT
