There is an error because you told MMPBSA.py not to strip out the waters
from the trajectory (strip_mdcrd=0), but your receptor and ligand masks do
not include any water residues. Are you wanting to include the 10 water
molecules in the binding calculation or not? If you don't want to include
them, then just change strip_mdcrd to 1 and re-run the calculation. If you
want to include the waters, then either your ligand or receptor topology
files need to have those waters present, with the corresponding residues
being defined in either the receptor_mask or ligand_mask.
I hope that helps.
-Bill
On Tue, Aug 24, 2010 at 7:53 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> I have an input trajectory (PPLW10), such that P=protein,P=peptide,L=ligand
> and W10=10 waters. My task is to do binding energy calculation using
> mmpbsa.py.
>
> Note:
> Protein=1-187
> Peptide=188-199
> Ligand=200
> Water=201-210
>
> My input script:
> -------
> &general
> verbose=2, interval=1, strip_mdcrd=0,
> receptor_mask=':1-187:188-199', ligand_mask=':200',
> /
> &gb
> igb=5, saltcon=0.100
> /
>
> EOF
>
> # Execute the program
> $DO_PARALLEL $EXE -O -i mmpbsa.in \
> -cp ../PPLW10.prmtop \
> -rp ../PP.prmtop \
> -lp ../L.prmtop \
> -y ../close.mdcrd \
> -o FIN.out \
>
> -------
>
> Note: L.prmtop contain only the atoms for the ligand, without water. The
> PPLW10.prmtop contains solute (protein+peptide+ligand) and solvent (10
> waters).
>
> After I did MMPBSA.py, below is the error from file.out:
> ----
> Starting gb calculation...
>
> calculating ligand contribution...
> calculating receptor contribution...
> calculating complex contribution...
>
> Calculations complete. Writing output file(s)...
>
> Traceback (most recent call last):
> File "/usr/local/amber10_serial/amber10/bin/MMPBSA.py", line 1397, in
> <module>
> decompout, idecomp, dec_verbose, ligstart, decomprun, surften,
> cavity_surften, temp)
> File "/mnt/home/local/amber10_serial/amber10/src/mmpbsa_py/utils.py",
> line 4595, in PrintFinalResults
> '',finaloutput, debug, numframes, one_trajectory,verbose) # noalascan
> is [avg,stdev] for total DELTA G
> File "/mnt/home/local/amber10_serial/amber10/src/mmpbsa_py/utils.py",
> line 1754, in gboutput
> bonddif[x] = bonddif[x] - bond[x]
> IndexError: list index out of range
> ----
>
> And, I checked the _MMPBSA_*mdout files:
>
> MMPBSA_ligand_gb.mdout
> -------
> BOND = 12.8698 ANGLE = 52.2840 DIHED =
> 43.8086
> VDWAALS = -12.0174 EEL = 713.3568 EGB =
> -607.9146
> 1-4 VDW = 8.3908 1-4 EEL = -887.6609 RESTRAINT =
> 0.0000
> ESURF = 4.8120
> minimization completed, ENE= -.67207087E+03 RMS= 0.210204E+02
> -------
> It looks fine to me.
>
> But, the MMPBSA_receptor_gb.mdout
> ---
> BOND = 16559590.1778 ANGLE = 290768.1866 DIHED =
> 10659.1550
> VDWAALS = 11518920.7677 EEL = -4590.3634 EGB =
> -4515.0725
> 1-4 VDW = 3577068.6287 1-4 EEL = 412.9539 RESTRAINT =
> 0.0000
> ESURF = 91.7749
> minimization completed, ENE= 0.31948406E+08 RMS= NaN
> ----
> There is a problem in receptor.
>
> And, finally MMPBSA_complex_gb.mdout
> ----
> BOND = 640.6054 ANGLE = 1594.2719 DIHED =
> 2076.8421
> VDWAALS = -1678.6856 EEL = -14017.8454 EGB =
> -2941.7994
> 1-4 VDW = 767.4366 1-4 EEL = 6808.5420 RESTRAINT =
> 0.0000
> ESURF = 87.9797
> minimization completed, ENE= -.66626527E+04 RMS= 0.181731E+02
> ----
>
>
>
> Is the input file for mmpbsa.py correct ? I know there are ten water
> molecules in the complex (PPLW10.prmtop), and am not sure how to specify it
> so the script can recognize it. Even if there is no problem calculating with
> waters, I can not find the cause why there is index error problem.
>
>
> Amor
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Aug 24 2010 - 05:30:03 PDT
