You will need to run ante-MMPBSA.py to create the prmtop files that
correspond to your new definitions of receptor and ligand. Because you need
prmtop files that correspond to each of them. So you do not need to re-run
the simulations, but just use ante-MMPBSA.py to create the prmtop files you
need for the new MMPBSA.py calculation.
-Bill
On Wed, Nov 8, 2023 at 9:51 AM VERONICA MARTIN HERNANDEZ via AMBER <
amber.ambermd.org> wrote:
> 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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Wed Nov 08 2023 - 09:30:03 PST
