fkaiserbio
commented
3 years ago Thanks for the detailed report! Single protonated states are obviously not considered during detection at the moment. The decision has to be implemented in these lines of code:
Hello,
Describe the bug currently I was analysing a protein-small ligand complex and recognised that a salt bridge was detected even thought it should not.
In particular, the compound (carboxylate group) is forming a salt bridge with residue H440 (see attached PDB file), however, this residue is single protonated and thus should not form a salt bridge.
To Reproduce I used both the webserver and the command-line tool. Regarding the command-line tool I used the following command:
sudo docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f -tvy --nohydro --maxthreads 20
Expected behavior In this example, I would expect a hydrogen bond. However, as described by PLIP either a hydrogen bond or a salt bridge is reported. Therefore, I am suggesting that once the problem is fixed, a hydrogen bond would be detected.
Desktop (please complete the following information):
Thanks in advance!
I used the subsequent PDB-file: 6kb3_GitHub.txt