index 40 is out of bounds for axis 0 with size 40

[sanasaeed]

I am calculating binding free energy of Protein ligand complex, 41 lambdas. i got this error.
Traceback (most recent call last):
File "/share/anaconda2/bin/alchemical_analysis.py", line 4, in
import('pkg_resources').run_script('alchemical-analysis==1.0.2.dev0', 'alchemical_analysis.py')
File "/share/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/share/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py", line 1226, in
main()
File "/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py", line 1212, in main
totalEnergies()
File "/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py", line 583, in totalEnergies
dF[name] += df_allk[k][name]
IndexError: index 40 is out of bounds for axis 0 with size 40

[davidlmobley]

Can you please provide a link to your input (i.e. share a tarball of the
.xvg files via GitHub or similar)?

Thanks.

On Sun, Apr 24, 2016 at 11:16 PM, Sana Saeed [email protected]
wrote:

I am calculating binding free energy of Protein ligand complex, 41
lambdas. i got this error.
Traceback (most recent call last):
File "/share/anaconda2/bin/alchemical_analysis.py", line 4, in
import('pkg_resources').run_script('alchemical-analysis==1.0.2.dev0',
'alchemical_analysis.py')
File
"/share/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/
init.py", line 726, in run_script
File
"/share/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/
init.py", line 1484, in run_script
File
"/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py",
line 1226, in
main()
File
"/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py",
line 1212, in main
totalEnergies()
File
"/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py",
line 583, in totalEnergies
dF[name] += df_allk[k][name]
IndexError: index 40 is out of bounds for axis 0 with size 40

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#87

David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
[email protected]
work (949) 824-6383
cell (949) 385-2436

[sanasaeed]

https://www.dropbox.com/s/csdf8v59z5cmqh5/complex.zip?dl=0

[sanasaeed]

i have sent you the dropbox link, can you see it? Sana Saeed Khan,Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.

On Tuesday, April 26, 2016 12:31 AM, David L. Mobley <[email protected]> wrote:

Can you please provide a link to your input (i.e. share a tarball of the
.xvg files via GitHub or similar)?

Thanks.

On Sun, Apr 24, 2016 at 11:16 PM, Sana Saeed [email protected]
wrote:

I am calculating binding free energy of Protein ligand complex, 41
lambdas. i got this error.
Traceback (most recent call last):
File "/share/anaconda2/bin/alchemical_analysis.py", line 4, in
import('pkg_resources').run_script('alchemical-analysis==1.0.2.dev0',
'alchemical_analysis.py')
File
"/share/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/
init.py", line 726, in run_script
File
"/share/anaconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/
init.py", line 1484, in run_script
File
"/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py",
line 1226, in
main()
File
"/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py",
line 1212, in main
totalEnergies()
File
"/share/anaconda2/lib/python2.7/site-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/EGG-INFO/scripts/alchemical_analysis.py",
line 583, in totalEnergies
dF[name] += df_allk[k][name]
IndexError: index 40 is out of bounds for axis 0 with size 40

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Reply to this email directly or view it on GitHub
#87

David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
[email protected]
work (949) 824-6383
cell (949) 385-2436
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