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Hello,
I’ve started studying molecular dynamics where I have a transmembrane protein that I want to be covalently bond to a ligand (MC-Val-Cit-Doxorubicin). I performed docking between the ligand to the protein and built a bond between them ( C2 maleimide of the ligand binds to the cysteine, CYS150, of the protein). Forward, I built the system in CHARMM-GUI and extracted the files that will serve as input for gromacs. However, in CHARMM I lose the covalent bond of the ligand to the protein, because there is a ‘Bond order error’. How can I get around this problem?
Regards,
Rafael