Re: [AMBER] nmode list index out of range

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 11 Apr 2012 15:00:23 -0400

Have you applied all bug fixes? I think a fix was posted for this a few months ago. If not, I will dig the fix up and post it tomorrow.

Note, this issue should be fixed in AmberTools 12 which you can download now on ambermd.org

HTH,
Jason 

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 11, 2012, at 9:34 AM, manikanthan bhavaraju <manikanthanbhavaraju.gmail.com> wrote:
> 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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> AMBER.ambermd.org
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Received on Wed Apr 11 2012 - 12:30:05 PDT
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