AMBER Archive (2009)

Subject: [AMBER] Using GAFF with a covalently bound ligand or label

From: Sale, Kenneth L (klsale_at_sandia.gov)
Date: Wed Jan 07 2009 - 19:30:10 CST

I would like to simulate proteins to which a covalently bound label (i.e.
cross-linker, spin label, fluorescent probe) has been attached at the SG of
a cysteine. I am thinking that the best approach is to use a standard AMBER
FF for the protein and the GAFF for label. My questions are: 1) does this
make sense? and 2) if so, how do I treat the SG to label connection? I
assume I will have to add a few FF parameters to deal with this, but can
this be done across two FFs with different atom type nomenclature?

Thanks,
Ken

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