gmx_MMPBSA

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[Question]: unknown error when installing gmx_MMPBSA

1

### My Question is... Dear users, I tried to install gmx_MMPBSA using conda/pip in Centos (shell: zsh). After using command "$ screen" and then in screen I ran "$ conda...

leiqian-nmsu

[Bug-gmx_MMPBSA]: Bug in gmx_MMPBSA: Alanine scanning

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### Bug summary Tried to use gmx_MMPBSA: Alanine scanning function to mutate a residue (on the interface of two proteins) to Alanine. But it could not work. ### Terminal output...

leiqian-nmsu

[Bug-gmx_MMPBSA]: Error Parsing results to output files

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### Bug summary Failed to parse results to output files ### Terminal output ```bash "[INFO ] Cleaning normal complex trajectories... [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO...

kolmorgan

[ENH]: add 3D-RISM-AI

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### In which tool? gmx_MMPBSA ### New Feature https://github.com/IkeguchiLab/3D-RISM-AI https://pubs.acs.org/doi/full/10.1021/acs.jpcb.2c03384 ### Description _No response_ ### Relevance low ### Difficulty to implement _No response_

marioernestovaldes

[Bug-gmx_MMPBSA]: KeyError:"ie"

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### Bug summary When I was calculating my protein-ligand complex, an error occurred during the processs ### Terminal output ```bash File "/home/yxp212121/yxp/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/yxp212121/yxp/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 112,...

WXYWD

[Question]: No module name parmed

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### My Question is... Hi, I installed gmx-MMPBSA and was trying to run the "gmx_MMPBSA_test". This error showed up:

Brandt84

[Question]: Positive Binding Energy

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### My Question is... How can I avoid calculating ΔEDISPER term when performing a CHARMMFF pbsa calculation? I found a solution: https://groups.google.com/g/gmx_mmpbsa/c/pYeE20pbhnc?pli=1 however, I still don't know how to discard...

laiyii

TypeError: unhashable type: 'list'

3

### Bug summary I've exported my folder from the HPC server and run gmx_MMPBSA_ana on my linux virtual machine. Recently, with larger frame runs (I ahve 3000 frames for 30...

bee-wulf

[ENH]: Add progress bar and estimated time to calculations

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### In which tool? gmx_MMPBSA ### New Feature Add progress bar and estimated time to calculations ### Description Sometimes the uncertainty of not knowing how the calculation is progressing can...

Valdes-Tresanco-MS

CalcError: /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj failed with prmtop COM.prmtop!

3

### Bug summary i ran a NAMD simulation and converted the files to GROMACS to be able to use gmx_MMPBSA and started the calculation with &gb and QH entropy, however,...

hima111997