-
### My Question is...
I want to use gmx_MMPBSA to analyse a protein-protein complex where the receptor is embedded in a lipid bilayer. I've used the CHARMM36 ff for the simulations, and followed your…
-
### My Question is...
gmx_MMPBSA reported: .conda/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:650: GromacsWarning: angles funct != 1 or 5; unknown functional warnings.…
C0921 updated
11 months ago
-
### My Question is...
I am encountering an issue while using gmxMMPBSA to process a trajectory of a protein-ligand-membrane protein. The ligand contains LPH, so I followed the tutorial to handle it. …
-
### Documentation Link
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/analyzer/
### Problem
In several cases, `set cartoon_side_chain_helper, 1` causes undesired visual effects, e.g. it shows …
-
### My Question is...
when i use the following command to mutate A/127 ARG by ALA, I meet the error above at Loading and checking parameter files for compatibility...
-
### Bug summary
I'm looking at the interaction between two domains of the same protein, split by the index file. The trajectory is 15,000 frames. I've loaded the decomp and energy for complex, recept…
-
### My Question is...
What to do when you get this error:
Checking external programs...
[ERROR ] MMPBSA_Error Could not find necessary program [cpptraj].
Check the gmx_MMPBSA.log fil…
-
### My Question is...
Hello, I've encountered a significant discrepancy in the results of binding free energy calculations when using two different versions of gmx_mmpbsa. Version Details: Using v…
-
### Bug summary
Hi,I calculate a system with LPH followed the tutorial,but it occur bad atom type error (bad atom type :IG) when program calculate complex contribution.
### Terminal output
```bash
…
-
### My Question is...
**I executed protein ligand MD simulation using Gromacs. Now i want to study water placement using 3DRISM. But it return following error "CHAMBER prmtops cannot be used with 3…