-
### Server Implementation
Paper
### Server Version
1.17.1
### CombatLogX Version
[11:54:54 INFO]:
[11:54:54 INFO]: Java Version: 17
[11:54:54 INFO]: Java Vendor: Oracle Corporation
[11:54:54 I…
-
-
Hi, I want to build a protein-ligand system where the ligand has more than 150 atoms.
Here is my script:
```
def read protein(protein_file):
protein = pdbfile.PDBFile(protein_file)
retu…
-
I was trying to parametrize a protein with a TPO residue, but I encountered an error. Could you please help me?
[protein_prep.txt](https://github.com/user-attachments/files/16683847/protein_prep.tx…
-
-
Hi all,
I tried changing to different gaff versions. Just for starters, I hardcoded one.
```
rbfe_settings.forcefield_settings.small_molecule_forcefield='gaff-2.11'
```
There was no issue…
-
Error during installation according to [this guide](https://carlesperez94.github.io/frag_pele/installation.html):
```
conda create -n frag python=3.7 --yes
source activate frag
git clone https:/…
-
Hi,
I'm trying to use `Molly.jl` to reproduce some of the work I have done in `Gromacs`, however, it raises error in `System` building stage.
Specifically, I use the following `Gromacs` commands t…
-
-
While writing the code as per the [User's Guide](https://isicle.readthedocs.io/en/latest/user_guide/NMR.html) for NMR Chemical Shift Calculation in CREST Conformational Ensembles , there is a runtime…