AMBER Archive (2006)

Subject: Re: AMBER: Charges from NMR spin densities

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 27 2006 - 10:57:32 CST

On Thu, Jan 26, 2006, David LeBard wrote:
>
> I would like to know if it is possible to use atomic charges determined
> experimentally from NMR spin densities within my protein's active site?

If you want to use non-standard charges (derived however you please), you
will need to give the residues near the active site special residue names (to
distinguish them from the rest of the protein.) Then, in LEaP, copy the
regular residue to the new name, and edit the new-name one, entering the
charges you want. Then if you load your modified pdb file in, the residues
with altered names will get your special charges.

...good luck...dac

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