How to preserve the input ligand's coordinates?

[Lin Min Htoo]

Hello,

I am using gypsum-DL to correctly ionise ligands that already have the correct coordinates (eg co-crystal ligand from RCSB or docked ligand). However, even with these flags, the output ligand's coordinates are reset, and it is both a translation & rotation of the input ligand. This is a problem as the ligand's coordinates need to be correct with respect to the protein pocket. I did not find any flag in gypsum-DL to preserve the ligand coordinates.

Would you have any ideas on this issue?

[Jacob Durrant]

Hi Lin,

Thanks for reaching out and expressing your interest in Gypsum-DL. I appreciate your feedback. It's a known limitation of the program, unfortunately. Our initial focus in creating Gypsum-DL was to prepare ligands for docking, so changing ligand coordinates didn't matter so much. But your use case is also perfectly reasonable.

I recommend using a program like Open Babel, which allows you to protonate ligands at a specific pH. I believe Open Babel's -H flag does a pretty good job, and it doesn't change the atomic coordinates.

I hope this suggestion helps! All the best.

[Author]

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