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### Bug summary
Hi, I am unable to understand what is wrong with my input. It stated that 1 water/ion molecule was found, but there isn't any. I had ran gmx_MMPBSA on a different complex (same protei…
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### My Question is...
I can't selecting Proline and Glycine when I run Alanine scanning.
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These are the things we have to check/do:
- [ ] Tan & Luo radii implementation. Currently, when the `radiiopt` is set to 0, the radii defined by the user is used. Although it may be common, we should…
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In the final step, I faced with the following error, can you help me figure out my problem?
Error: Error(s) occurred during execution.
File "/usr/local/bin/MMPBSA.py", line 99, in
app.fil…
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### My Question is...
How to Remove ligand from Decomposition analysis. In the graph along with receptor residues, ligand is also coming. Thanks
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Hi
I am trying to calculate the mmpbsa between a protein and DNA. I use the following command
gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 15 -ct md.xtc
However, it gives me this erro…
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### Bug summary
In a very very rare case, the square root seems fail for the negative number, ends up with the `ValueError: math domain error`. This particular formula looks like the absolute value…
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### Is there a way to monitor the progress?
The g_mmpbsa had a workaround where plotting the xvg file being generated gave an idea about the progress of the calculations. So, is there any way we coul…
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### In which tool?
gmx_MMPBSA
### New Feature
Give the path to our Gromacs executable or give a suffix to gmx_MMPBSA command line argument.
### Description
I have to manage several versions of Gr…
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### My Question is...
Hi all,
I know that the energies achieved via mmpbsa calculations from different tools are not necessarily comparable between different tools. However, I was very suprised …