-
### In which tool?
gmx_MMPBSA
### New Feature
Currently qmmask selection is based on full residues, either directly via residue number or within specific distance of the ligand.
Additional optio…
-
### 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 | …
-
### 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…
-
### 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…
-
### 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…
-
Hii
I was installing gmx_mmpbsa and ran into this problem.
Kindly help.
sudo pip3 install gmx-MMPBSA
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version …
-
### Bug summary
Conducting MMPBSA calculations fails on COM.prmtop for some reason. MMGBSA proceeds to completion without issue. Looking in the _GMX_complex_pb.out it seems there's something off wi…
-
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:
~~~~~~~~~~~~~~~…
-
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…
-
### My Question is...
gmx_mmpbsa -O -i MMGBSA.in -cs ../md_100.tpr -ct ../md_100.xtc -ci ../index.ndx -cg 3 4 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv WARNING: No ICD…