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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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NameError: global name 'parametersB' is not defined #37

Closed camizanette closed 9 years ago

camizanette commented 9 years ago

I was using a different format of topologies files and I got this error saying the variable parametersB is not defined previously. The issue comes from Part IV, when it is processing the dihedrals and the top file format doesn't match with what the code is expecting, going to an exception in line 380. What I have noticed is acpype and parmed return different dihedrals functions types (9 and 1), and amb2gmx.pl returns the function type 3 (the one that works). I can provide samples in case it is necessary.

Traceback (most recent call last): File "../../local/alchemical-setup-master/alchemical-setup.py", line 549, in buildBonded() # Part IV. File "../../local/alchemical-setup-master/alchemical-setup.py", line 429, in buildBonded postprocessDihedrals() File "../../local/alchemical-setup-master/alchemical-setup.py", line 385, in postprocessDihedrals if l['parameters'][-1] != parametersB[-1]: NameError: global name 'parametersB' is not defined

davidlmobley commented 9 years ago

Yes, please provide a link to input files to reproduce the problem.

Thanks.

On Mon, Nov 2, 2015 at 10:04 PM, camizanette notifications@github.com wrote:

I was using a different format of topologies files and I got this error saying the variable parametersB is not defined previously. The issue comes from Part IV, when it is processing the dihedrals and the top file format doesn't match with what the code is expecting, going to an exception in line 380. What I have noticed is acpype and parmed return different dihedrals functions types (9 and 1), and amb2gmx.pl returns the function type 3 (the one that works). I can provide samples in case it is necessary.

Traceback (most recent call last): File "../../local/alchemical-setup-master/alchemical-setup.py", line 549, in buildBonded() # Part IV. File "../../local/alchemical-setup-master/alchemical-setup.py", line 429, in buildBonded postprocessDihedrals() File "../../local/alchemical-setup-master/alchemical-setup.py", line 385, in postprocessDihedrals if l['parameters'][-1] != parametersB[-1]: NameError: global name 'parametersB' is not defined

— Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/37.

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

camizanette commented 9 years ago

Here is the dropbox link https://drive.google.com/folderview?id=0B5Hiv4aw8v8CWWU3N2ZVb2FsbWs&usp=sharing

There are two folders, one with topologies from Parmed and other from amb2gmx.pl.

Let me know if it does not work.

Thanks!

davidlmobley commented 9 years ago

Oops, this is an issue for alchemical-setup, yes?

Thanks.

On Tue, Nov 3, 2015 at 4:18 PM, camizanette notifications@github.com wrote:

Here is the dropbox link https://drive.google.com/folderview?id=0B5Hiv4aw8v8CWWU3N2ZVb2FsbWs&usp=sharing

There are two folders, one with topologies from Parmed and other from amb2gmx.pl.

Let me know if it does not work.

Thanks!

— Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/37#issuecomment-153531580 .

David Mobley dmobley@gmail.com 949-385-2436

camizanette commented 9 years ago

Ops. I just posted on the right place.