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### Bug summary
My system only contains proteins(Chain A, Chain B and Chain C) water and ions. I'm attempting to compute the binding energy of Chain C binding to Chain A-Chain B complex. I utilized…
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### My Question is...
/tmp/pip-build-env-8i30r4s1/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h:139:62: note: in definition of macro ‘PyArray_GETPTR1’ 139 | …
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Hi Hai,
I think I've installed everything to be able to use the pytraj module. Could you send me an example script to import a PDB (instead of the .nc and .parm7 files) in pytraj, score it, and acces…
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Hi,
I am using the FreeEnergyPlot.py script to analyze per-residue energy decomposition for my protein-ligand complex. However, I noticed that the energy component graphs for the complex (delta_energ…
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Hi everyone,
In this project, we have a bunch of experimental data on the binding of small molecules to WDR91. Many of the molecules are in nice matched pairs, in which the molecules differ by a si…
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### Bug summary
When I execute the an mmgbsa run, the run proceeds through calculating the complex, receptor and ligand contributions, but then fails at "Parsing results to output files..." saying th…
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**Describe the bug**
We have omega (but not omega toolkit) and oequacpac license. In this condition, openeye license check is not done correctly.
**To Reproduce**
```python
from openmm.app import …
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### Bug summary
When running for other complex its working for few system not working giving following error.
I run some MD simulation with Gromacs 2023 for them its working. The md simulation exe…
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This protocol is excellent to the new bees like me.
However, I need little more support.
I would like to run the MMPBSA after this run.
For that, it is required to add index file.
Kindly guide…
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When i want to calculate MMGBSA with rgbmax=10.0, i got an error:
InputError: Unknown variable rgbmax in &gb.
i dont know why i can't use rgbmax in &gb.
Here are the outputs below:
~~~~~~~~~~~~~~~…