AMBER Archive (2009)

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

From: Markus Kaukonen (
Date: Fri Jan 16 2009 - 00:31:53 CST

This might help for a more laborous solution:

On Thu, Jan 8, 2009 at 3:30 AM, Sale, Kenneth L <> wrote:
> 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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