[AMBER] MMPBSA.py indexError

From: Amor San Juan <amorsanjuan.yahoo.com>
Date: Tue, 24 Aug 2010 04:53:30 -0700 (PDT)

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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Received on Tue Aug 24 2010 - 05:00:10 PDT