[AMBER] problem with MMPBSA.py (and/or ante-MMPBSA.py)

From: Artur Hermano via AMBER <amber.ambermd.org>
Date: Tue, 4 Oct 2022 12:55:34 +0000

Dear Amber users,

I am trying to use run free energy calculations using ante-MMPBSA.py + MMPBSA.py in a system consisting of protein+calcium ion+glycan bound to small peptide+water+counterions(Na and Cl). I want to estimate the free energy of binding between the protein and the ligand (glycan+peptide), but there are a few odd things happening that make me think I must be missing something:

  1.
when I use ante-MMPBSA.py, my command line is: ante-MMPBSA.py -p sys.prmtop -c complexWT.prmtop -r receptorWT.prmtop -l ligandWT.prmtop -s .8988-37750 -m :1-562, where
 atoms 8988 to 37750 are waters, sodium and chloride ions, and none of them is actually removed, because all .prmtop files generated have SOD, CLA and many O H1 H2 which correspond to waters... the only way to truly remove them is to do: ante-MMPBSA.py -p sys.prmtop -c complexWT.prmtop -r receptorWT.prmtop -l ligandWT.prmtop -s :WAT,:SOD,:CLA -m :1-562, and then I do not see any SOD, CLA or O H1 H2 in the generated .prmtop files, but...

  2.
when I run MMPBSA.py with those .prmtop files, my run crashes within 6 minutes with the following error message: "CalcError: /opt/software/RI/apps/Amber/20.12-iomkl-2020.02-AmberTools-21.12/bin/sander failed with prmtop complexWT.prmtop!" and the three PDB files generated (_MMPBSA_ligand.pdb, _MMPBSA_receptor.pdb and _MMPBSA_complex.pdb)
  3.
all contain CLA and SOD ions!! How come they were not present in the .prmtop files, but still somehow managed to be present in the PDB files? I believe the error in my calculation arises from the fact that I am not supposed to have counterions in any of these structures... Can someone please help me figure out what is happening?

Below is my code and the input file for MMPBSA:

module purge
module load amber/20.12-iomkl-2020.02-ambertools-21.12

mpirun $AMBERHOME/bin/MMPBSA.py.MPI -O -i pbsa.in -o resultsPBSA_calnexWT.dat -sp sys.prmtop -cp complexWT.prmtop -rp receptorWT.prmtop -lp ligandWT.prmtop -y prodallWT.nc

pbsa.in
Input file for running PB and GB
&general
   startframe=1,endframe=10000, verbose=1,
   keep_files=0,entropy=1
/
&gb
 igb=5,
 saltcon=0.15
/
&pb
 istrng=0.15
/
&decomp
  csv_format=1,dec_verbose=3,
  idecomp=4,
/

Thank you very much in advance!!

Kind regards,
Artur
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Received on Tue Oct 04 2022 - 06:30:03 PDT
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