Dear Amber,
I came across an error when I calcultate free energy by MMPBSA,
.....
IndexError: list index out of range
Exiting. All files have been retained.
The followsing is the configuration of mmpbsa-2.in file
&general
startframe=1001, endframe=2000, interval=1,
verbose = 1
ligand_mask = ":1"
receptor_mask = ":2-299"
/
&gb
igb=8, saltcon=0.100,
/
&pb
inp=0, radiopt=0,
istrng=0.100,
/
&decomp
idecomp=2, print_res="1,14,20,35,38-39,77-80,83,84-86,88-89,146-148,177,187,196-197,201-202,205,243,271-272,275,2291,4798,5231,7029,7892,10373",
dec_verbose=3,
/
If I remove the following parameters, the mmpbsa is goes well, I wonder how to fix the issue.
&decomp
idecomp=2, dec_verbose=3,
print_res="1,14,20,35,38-39,77-80,83,84-86,88-89,146-148,177,187,196-197,201-202,205,243,271-272,275,2291,4798,5231,7029,7892,10373",
/
Any suggestion will be much appreciate.
ligand：1
protein：2-299
print_res:"the amino acid residue within 5 angstrom around ligand"
MMPBSA.py -O -i mmpbsa-2.in -o FINAL_RESULTS_MMPBSA-2.dat -do FINAL_DECOMP_MMPBSA-2.dat -sp complex_solv.prmtop -cp EstJ6-DBP-now.prmtop -rp EstJ6-now.prmtop -lp DBPH-now.prmtop -y eq_density-2.nc > qjr_mmgbsa-2.log
complex_solv.prmtop：protein-ligand-water
EstJ6-DBP-now.prmtop ：protein-ligand complex
EstJ6-now.prmtop：protein
DBPH-now.prmtop：ligand
Zhihong Xin
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Received on Mon Mar 08 2021 - 04:30:02 PST
