gmx_MMPBSA: Value Error

Sri Cheerala Vijay Sai Krishna, Doctoral Research Scholar, Chemistry, SSSIHL

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Mar 27, 2023, 5:10:02 AM3/27/23

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Hello Sir,

Can you just helm me with this error.

***************************************************************************************

[INFO ] Cleaning normal complex trajectories...
[INFO ] Building AMBER topologies from GROMACS files... Done.

[INFO ] Loading and checking parameter files for compatibility...
[INFO ] Preparing trajectories for simulation...

[INFO ] 101 frames were processed by cpptraj for use in calculation.
[INFO ] Starting calculations in 1 CPUs...

[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /home/research/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
100%|####################| 101/101 [elapsed: 10:37 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|####################| 101/101 [elapsed: 10:19 remaining: 00:00]
[INFO ] calculating ligand contribution...
100%|####################| 101/101 [elapsed: 00:05 remaining: 00:00]
[INFO ] Parsing results to output files...

File "/home/research/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
app.parse_output_files()
File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1211, in parse_output_files
self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
AmberOutput._read(self)
File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
self._get_energies(output_file)
File "/home/research/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 617, in _get_energies
self['BOND'][self.frame_idx] = float(words[2])
ValueError: could not convert string to float: '*************'
Exiting. All files have been retained.

*****************************************************************

gmx_MMPBSA.log

Mario Ernesto

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Mar 27, 2023, 9:47:07 AM3/27/23

to Sri Cheerala Vijay Sai Krishna, Doctoral Research Scholar, Chemistry, SSSIHL, gmx_MMPBSA

Please, check this section in the docs https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions

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Sri Cheerala Vijay Sai Krishna, Doctoral Research Scholar, Chemistry, SSSIHL

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Mar 27, 2023, 1:03:34 PM3/27/23

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When I tried the gmx_MMPBSA_test, all the tests were showing errors.

******************************************************************

gmx_MMPBSA_test
[INFO ] Cloning gmx_MMPBSA repository in /home/vijaysai/gmx_MMPBSA_test
Cloning into '/home/vijaysai/gmx_MMPBSA_test'...
remote: Enumerating objects: 21359, done.
remote: Counting objects: 100% (2191/2191), done.
remote: Compressing objects: 100% (502/502), done.
remote: Total 21359 (delta 1292), reused 2147 (delta 1261), pack-reused 19168
Receiving objects: 100% (21359/21359), 334.66 MiB | 535.00 KiB/s, done.
Resolving deltas: 100% (14844/14844), done.
Updating files: 100% (697/697), done.
[INFO ] Cloning gmx_MMPBSA repository...Done.
[INFO ] Example STATE
--------------------------------------------------------------------------------
[INFO ] Protein-Ligand (Single trajectory approximation) RUNNING
[ERROR ] Protein-Ligand (Single trajectory approximation) [ 1/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log)
[INFO ] Protein-Protein RUNNING
[ERROR ] Protein-Protein [ 2/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Protein_protein/4.log)
[INFO ] Protein-DNA RUNNING
[ERROR ] Protein-DNA [ 3/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Protein_DNA/5.log)
[INFO ] Protein-Glycan RUNNING
[ERROR ] Protein-Glycan [ 4/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Protein_glycan/7.log)
[INFO ] Comp_receptor RUNNING
[INFO ] Comp_receptor [ 5/ 9] DONE
[INFO ] Alanine Scanning RUNNING
[ERROR ] Alanine Scanning [ 6/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Alanine_scanning/12.log)
[INFO ] Stability calculation RUNNING
[ERROR ] Stability calculation [ 7/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Stability/13.log)
[INFO ] Decomposition Analysis RUNNING
[ERROR ] Decomposition Analysis [ 8/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Decomposition_analysis/14.log)
[INFO ] Interaction Entropy approximation RUNNING
[ERROR ] Interaction Entropy approximation [ 9/ 9] ERROR
Please, check the test log
(/home/vijaysai/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)

**********************************************************************************

Thank you.

Regards,

Vijay Sai.

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Mario Ernesto

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Mar 27, 2023, 1:47:23 PM3/27/23

to Sri Cheerala Vijay Sai Krishna, Doctoral Research Scholar, Chemistry, SSSIHL, gmx_MMPBSA

can you send one of these logs

/home/vijaysai/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log

for example?

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marioe911116

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Mar 28, 2023, 12:41:05 AM3/28/23

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This is a bug in the new version 1.6.0. that has been corrected in the development version. This doesn't interfere with the proper functioning of the program to perform the calculations...

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