Hi,
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>
outfile.write(str(nmodenorm))
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
&general
endframe= 10, keep_files=2,
/
&nmode
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?
mani
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Wed Apr 11 2012 - 07:00:04 PDT
