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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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I want to estimate distance using chain id. So, i have tried the following input:
distance K210A-E97D **::A:;210@NZ,HZ1,HZ2,HZ3 ::D:;97@OE1,OE2,CD** out rgs01-salt-210-lys-97-glu-1.dat
ACTION S…
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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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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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Hi Harut,
How are you?
I'm trying to use iPBSA with CYP450 and quercetin, the ligands are ok, but MMPBSA has problems with heme group from CYP450.
Do you know how to do MMPBSA calculate the free en…
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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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### 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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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…