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MobleyLab / alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations
MIT License
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index 40 is out of bounds for axis 0 with size 40 #87

Open sanasaeed opened 8 years ago

sanasaeed commented 8 years ago

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 commented 8 years ago

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 notifications@github.com 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

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/87

David Mobley Associate Professor Department of Pharmaceutical Sciences Department of Chemistry 3134B Natural Sciences I University of California, Irvine Irvine, CA 92697 dmobley@uci.edu work (949) 824-6383 cell (949) 385-2436

sanasaeed commented 8 years ago

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

sanasaeed commented 8 years ago

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 <notifications@github.com> 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 notifications@github.com 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

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/87

David Mobley Associate Professor Department of Pharmaceutical Sciences Department of Chemistry 3134B Natural Sciences I University of California, Irvine Irvine, CA 92697 dmobley@uci.edu work (949) 824-6383 cell (949) 385-2436 — You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub