[AMBER] nmode list index out of range

From: manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Wed, 11 Apr 2012 08:34:46 -0500

I am performing nmode analysis for protein-ligand system for 2 frames.
The complex, receptor, and ligand got minimized but deltaS values are
not written to the output file. The progress.log file is showing the
following error

Beginning nmode calculations with mmpbsa_py_nabnmode...
Calculating normal modes for 2 frames

  calculating complex contribution for frame 0
  calculating receptor contribution for frame 0
  calculating ligand contribution for frame 0
  calculating complex contribution for frame 1
  calculating receptor contribution for frame 1
  calculating ligand contribution for frame 1
Traceback (most recent call last):
  File "/home/srg/mhb75/Download/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py",
line 1343, in <module>
  File "/home/srg/mhb75/Download/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py",
line 2263, in __str__
    totavg, totstdev = self.AvgStdev()
  File "/home/srg/mhb75/Download/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py",
line 2302, in AvgStdev
    stdev = self._tot_stdevs()
  File "/home/srg/mhb75/Download/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py",
line 2319, in _tot_stdevs
    sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]
IndexError: list index out of range
progress.log lines 1-27/27 (END)

input file:
Input file for running entropy calculations using nmode
   endframe= 10, keep_files=2,
 nmstartframe=1, nmendframe=10,
   nminterval=5, nmode_igb=1, nmode_istrng=0.1,

I have seen the amber archive for the solution but couldn't find any
help. Does anyone know how to address the issue?


Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
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Received on Wed Apr 11 2012 - 07:00:04 PDT
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