Hi
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
&general
startframe=200,
endframe=201,
receptor_mask=":1-381,406,408-1547",
ligand_mask=":382-405,407"
keep_files=2,
/
&gb
igb=2,
saltcon=0.100,
/
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>
app.loadcheck_prmtops()
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
Verónica
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 08 2023 - 08:00:02 PST
