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
