From: VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org>
Date: Wed, 8 Nov 2023 15:45:12 +0000


I just wanted to ask a question about MMPBSA

I have run a MD of a structure with 3 protein chains and a ligand and I have ordered in the pdb first the proteins and then the ligand. But now I want to study the interacion between the chain A ( which is formed for the residues 1-381, the residue 406, and the residues 408-1547) an the chain C (whic is formed for the residues 382-405 and 407). The script that I have used in MMPBSA.py is:

Input file for running PB and GB

and the comand is: $AMBERHOME/bin/MMPBSA.py -O -i mmgbsa.in -o FINALMMPBSA_structureY7S_SALL4.dat -sp structure-Y7S-solv.prmtop -cp structure-Y7S-dry.prmtop -rp strcutrewoSALL4-Y7S-dry.prmtop -lp SALL4.prmtop -y structure-Y7S-NVT_2.mdcrd > progress.log 2>&1

But I've got the next error: Loading and checking parameter files for compatibility...
  File "/home/soft/Amber22/amber22/bin/MMPBSA.py", line 98, in <module>
  File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 650, in loadcheck_prmtops
    self.normal_system.Map(INPUT['receptor_mask'], INPUT['ligand_mask'])
  File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/parm_setup.py", line 132, in Map
    raise PrmtopError('mismatch in receptor mask and receptor prmtop')
PrmtopError: mismatch in receptor mask and receptor prmtop

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.

So I don't know what to do but I prefer not to run another MD because I have done 30 of them and all have the same error

Thanks in advice for the help
AMBER mailing list
Received on Wed Nov 08 2023 - 08:00:02 PST
Custom Search