Hi,
Please rectify the error that reads "
raise PrmtopError('Complex natom != receptor natom + ligand natom')" in the log file.
It seems your number of complex atoms is not equal to the receptor and ligand atoms.
Best,
Satyajit
________________________________
From: ABDELATIF MESSAOUDI via AMBER <amber.ambermd.org>
Sent: Friday, March 3, 2023 4:33:36 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Free energy simulation with the MMPBSA
Dear AMBER users,
I am trying to perform a free energy simulation with the MMPBSA method.
mpirun -np 2 MMPBSA.py -O -i mmgbsa5.in -cp SK.top -rp receptor.top -lp
ligand.top -y SK_c.mdcrd &
However I am receiving the following message
cmvar.lcmvar:~/+Abdel/SQ/+Analyse$ Loading and checking parameter files for
compatibility...
Loading and checking parameter files for compatibility...
File "/home/lcmvar/SOFT/amber22/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/home/lcmvar/SOFT/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py",
line 573, in loadcheck_prmtops
self.normal_system = MMPBSA_System(FILES.complex_prmtop,
File
"/home/lcmvar/SOFT/amber22/lib/python3.10/site-packages/MMPBSA_mods/parm_setup.py",
line 109, in __init__
self._validate()
File
"/home/lcmvar/SOFT/amber22/lib/python3.10/site-packages/MMPBSA_mods/parm_setup.py",
line 876, in _validate
raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
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.
File "/home/lcmvar/SOFT/amber22/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/home/lcmvar/SOFT/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py",
line 573, in loadcheck_prmtops
self.normal_system = MMPBSA_System(FILES.complex_prmtop,
File
"/home/lcmvar/SOFT/amber22/lib/python3.10/site-packages/MMPBSA_mods/parm_setup.py",
line 109, in __init__
self._validate()
File
"/home/lcmvar/SOFT/amber22/lib/python3.10/site-packages/MMPBSA_mods/parm_setup.py",
line 876, in _validate
raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
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.
Could someone suggest me an idea to solve this problem
Best regards
Abdelatif Messaoudi
LCMVAR, University of Batna1, Algeria
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Received on Thu Mar 02 2023 - 20:00:03 PST
