Dear Zhihong Xin,
It looks like your protein + ligand system has 299 residues. However,
you are referencing residue numers 2291, 4798 and so forth in your input
files. I presume they are water molecules; those are stripped from your
trajectory for MMPBSA analysis. Maybe you can give it a try modifying
this line:
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",
to:
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",
I hope it helps.
Best,
Mariano
On 08/03/2021 13:12, 辛志宏 wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Mariano Curti
Postdoctoral researcher - Romero Group
Institute of Chemical Research of Catalonia (ICIQ)
Av. Països Catalans 16 – 43007 Tarragona (Spain)
mcurti.iciq.es
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Received on Mon Mar 08 2021 - 04:30:03 PST
