AMBER Archive (2009)

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

From: David A. Case (
Date: Wed Jan 07 2009 - 20:42:27 CST

On Wed, Jan 07, 2009, 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?

What you propose makes some sense, depending on the nature of the
covalent connection. You would use the "bond" command in leap to add
the bond (formally, like a cross-link between two CYX residues).

The alternative would be to make a modified CYS-like residue that had
the label. This could be done with antechamber, perhaps with R.E.D. or
similar to get charges. In the end, this could be a distinction with
little or no difference, however.


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