[AMBER] »Ø¸´: Free energy simulation with the MMPBSA

From: Huang ZiJian via AMBER <amber.ambermd.org>
Date: Fri, 3 Mar 2023 04:17:52 +0000

Hi,

It seems like a common issue that you can search in the mailing list. Following Satyajit's comment, I think you could use ante-MMPBSA.py to generate protop files for MMPBSA.py. ( Details in AMBER mailing list: http://archive.ambermd.org/202302/0152.html ) And check the number of atoms carefully.

Hope this helps.

Best,
Zijian

________________________________
·¢¼þÈË: ABDELATIF MESSAOUDI via AMBER <amber.ambermd.org>
·¢ËÍʱ¼ä: 2023Äê3ÔÂ3ÈÕ 7:03
ÊÕ¼þÈË: AMBER Mailing List <amber.ambermd.org>
Ö÷Ìâ: [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 - 20:30:03 PST
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