[BUG] Protein parametrization fails if detects a disulfide bridge between reduced cysteine residues (CYS and not CYX)

[cespos]

Describe the bug
When using BSS.Parameters.parametrise() on a protein system, If BioSimSpace detects a disulfide bridge between cystein residues, it will add a "bond" command to the leap script:

However, if one or both cysteine residues forming the S-S bond are in the reduced state (-SH and not -S[-]), leap will fail to add the S-S bond.

Here is the leap error:

To Reproduce

import BioSimSpace as BSS

protein_coord = BSS.IO.readMolecules("test.pdb")[0]
protein = BSS.Parameters.parametrise(protein_coord, 'ff14SB', work_dir='leap')

Expected behavior

If BioSimSpace detects a S-S bond between reduced cysteines, it should:

• either do not add the S-S bond in the leap script and print a warning message for the user ("Detected potential disulfide bridge between CYS XXX and CYS XXX - check the input file preparation")
• or automatically delete the hydrogen atom bound to the sulfur atom from the cysteins.

The first option is preferable for me.

Input files
test.pdb

(please complete the following information):

• Ubuntu
• Version of Python: 3.10
• Version of BioSimSpace: 2023.3.0
• I confirm that I have checked this bug still exists in the latest released version of BioSimSpace: [yes/no] yes

[lohedges]

Thanks for reporting. Could you possibly upload the test.pdb file referenced in your issue so that I can debug?

[lohedges]

Hi again, any update on whether you are able to share a file for testing purposes?