AMBER Archive (2008)

Subject: Re: AMBER: standard residues

From: David A. Case (case_at_scripps.edu)
Date: Sat Mar 22 2008 - 11:30:03 CDT

On Wed, Mar 19, 2008, Holly Freedman wrote:

> I am modelling a protein with several subunits for which I would like
> to force incomplete valences with standard amino acid residues on the
> C-terminus of one subunit and on the N-terminus of another subunit; but for
> all the other termini I would like to use the regular terminal amino acids.
> Is this possible?

Yes. If the the amino acids are disjoint (e.g., you don't need both an
N-terminal GLY and and an incomplete GLY) you can edit the "addPdbResMap"
section from (a copy of) your leaprc file to specify what you want. You could
also just remove the addPdbResMap section, and specifically put the "N"
or "C" prefixes in your pdb file where appropriate.

...good luck...dac

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