GROMACS version: latest
GROMACS modification: Yes/No
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I want to cap my peptide by BOC and OME how can i do that?
Actually i am using charmm gui to generate files.
Can anyone please help??
What are BOC and OME? Are they supported by the force field? I can’t find anything in the CHARMM topology files so I suspect this simply isn’t an option.
BOC is tert-butoxycarbonyl protecting group and OME is oxy methyl
I don’t think BOC is even available in the CHARMM force field. The oxymethyl group should be. CHARMM-GUI will give you the available options for terminal patching; if they’re not there, they’re not in CHARMM and therefore can’t be used for simulations in GROMACS or anywhere else.