Using parent ligand for non-standard residues

User discussions
1

GROMACS version:2019
GROMACS modification: No
Dear all,

I need to do a molecular simulation for a protein (1EVQ PDB code) including non-standard MSE residue. Please let me know if I will have realistic results if I use its parent amino acid (MET) instead? The predefined force fields do not support the MSE.

Best regards,
Bahareh

2

Selenomethionine is often a non-biological substituent used to obtain better diffraction. You’ll have to investigate what was done to your particular protein, but perhaps the residue is natively MET instead of MSE.

3

Thank you very much!