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### Bug summary
Hi
I am trying to calculate the mmpbsa between a protein and a ligand with LPH atoms. After following this tutorial(https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/examp…
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### Bug summary
My topo and tpr file are generated by GMX2023 and gmx_MMPBSA, Can not output _GMXMMPBSA_COM_index.ndx.
I think this is a GMX issue, not gmx_MMPBSA.
### Terminal output
```bash
MMPB…
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I got some errors when i run gmx_MMPBSA_test
(gmx_MMPBSA v1.5.7 based on MMPBSA version 16.0 and AmberTools 20)
Here are the details:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CO…
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### Bug summary
I'm trying to perform MM/GBSA calculations with decomposition analysis.
My system is a metalloprotein (Mn2+) binding to an organic small ligand.
When decomposition with GB is perfo…
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### Bug summary
Hi there, I have an unnatural amino acid in my structure, and it reports an error when performing alanine scanning:
`MMPBSA_Error Selecting residue A:DASP:1 can't be mutated. Please,…
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### Bug summary
When using GROMACS 2023 to calculate the PBSA I get an error regarding making the ndx file. I installed the software using the conda environment and the env.yml file.
### Termina…
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### Bug summary
IndexError: string index out of range
### Terminal output
```bash
[INFO ] Loading and checking parameter files for compatibility...
File "/home/twg/miniconda3/envs/gmxMMPBSA/bin…
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### Bug summary
tleap failed when querying _GMXMMPBSA_leap.in
### Terminal output
```bash
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Changing the Complex residues name format f…
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### Bug summary
When performing decomposition with GB on a system with Mn, sander crashes with this error, `bad atom type: MN`
### Terminal output
```bash
NA
```
### gmx_MMPBSA.log
NA
### Opera…
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Hi I am running into the following fatal error:
Fatal error:
[DEBUG ] Index[2022] 2035 is larger than the number of atoms in the
[DEBUG ] trajectory file (2034). There is a mismatch in the con…