I'm new to Rosetta, and I'm currently attempting to create a params file for docking water as a secondary ligand in my docking experiment. I'm using the following Rosetta script for this purpose:
Rosetta/main/source/scripts/python/public/molfile_to_params.py -n X00 -pX00 --conformers-in-one-file 0001H2O.mol2 --keep-names --chain D
However, I'm encountering an error message that reads: "ValueError: No acceptable neighbor atoms in molecule!"
Interestingly, I had successfully employed the same script for generating the params file for my first ligand without any issues. Could you kindly provide any insights or suggestions to resolve this error?
Thank you for your assistance.
The mol2 file structure:
# Created by GaussView 6.0.16
1 O 0.5562 1.2256 -0.1126 O
2 H 1.5162 1.2256 -0.1126 H
3 H 0.2357 2.1305 -0.1126 H
1 1 2 1
2 1 3 1