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### Bug summary
gmx make_ndx failed when querying index_LIG.ndx
gmx make_ndx failed when querying index_final.ndx
### Terminal output
```bash
gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index_LI…
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I am facing a similar index out-of-range error when decomposing pairwise residue interactions between residues which are non-consecutive in sequence, for example, residues 12 and 14. However, it works…
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Hello, my output file just has complex total energy without ligand and receptor and so, without any delta calculations. Would you please tell me what the problem is, and how can I get ΔTOTAL and ΔG bi…
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### Bug summary
Hi, I ran protein-ligand MD simulations using gromacs with the OPLS-AA FF. When the ligand is a fatty acid, gmxMMPBA works fine, but when the ligand is another one, ChamberParm is not…
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### Bug summary
When using gmx_mmpbsa to calculate my protein-ligand trajectory(from gmx2023.3), the software seems can't read my topology correctly, which can be normally read by gmx.
### Terminal …
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### Bug summary
gmx_MMPBSA works normally. Running gmx_MMPBSA on mpi with mpirun just freezes the system after a while.
### Terminal output
```bash
[INFO ] Starting gmx_MMPBSA v1.6.2
[INFO ] …
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Hi,
I went through the tutorial in notebook for website, and everything is good. But when I download BioSimSpace, and ran in my local pc.
For the ABFE tutorial (04_fep/03_ABFE), it does not have "…
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### My Question is...
Hi sir, I would like to compute binding energy for my complex using mmpbsa module. However, when I tended to use sander.apbs typing sander_apbs=1 in &pb section, I got an error.…
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### My Question is...
Dear developer, I'm trying to use gmx_MMPBSA for analyzing MD simulations run by amber. If I'm looking through the files, e.g. parm_setup.py, my understanding is that GROMACS fi…
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### My Question is...
I am using gmxmmpbsa to claculate the free energy, but I get the following error: GromacsError: Only 3-point vsite type 1 is supported. Other systems can be calculated normall…