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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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but when I launch mmgbsa I have met this problem : bin/gmx editconf failed when querying com_traj.xtc.
Check the gmx_MMPBSA.log file to report the problem.
_Originally pos…
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I am trying to convert gromacs topology file to amber topology file to used MMPBSA or MMGBSA module of Amber Tool.
For this I used the following command
**parmed -p topol.top -O amb.parm7**
After r…
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### Bug summary
Overload CPU usage when using `rism3d.snglpnt`... same with sander? needs more tests...
### Terminal output
```bash
None
```
### gmx_MMPBSA.log
None
### Operating system
_No re…
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### Bug summary
150 ns MDS of I7L (MPXV) and Batefenterol (Chorine containing) was performed. The same MDS was performed with Burixafor and eluxadolin drug.
MMGBSA analysis gives errors with Batefe…
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[INFO ] Running calculations on normal system...
[INFO ] Beginning PB calculations with /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander
[INFO…
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Hi,
Here is a picture of the last weekly lint and tests:
![image](https://user-images.githubusercontent.com/30404086/196705259-6a187965-79de-47bf-8b73-60a08118d56e.png)
Errored Tests
❌ ChI…
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### Bug summary
i ran a NAMD simulation and converted the files to GROMACS to be able to use gmx_MMPBSA and started the calculation with &gb and QH entropy, however, the calculation stopped before fi…
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The values of bind free energr of protein-protein system are used to be positive, but change greatly after adjusting df slightly in the code. I have to say that the calculation result of this script i…
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I was following Protein_DNA_RNA_ion_ligand tutorial for MMPBSA calculation.
My system contains protein, RNA and DNA. I considered RNA_Protein as receptor and DNA as ligand and made the files accord…