AMBER Archive (2008)

Subject: Re: AMBER: standard residues

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Sat Mar 22 2008 - 17:27:07 CDT

Thank you Prof. Case. This is exactly what I needed to know. I am working on finding the binding
energy of one part of a protein with another part using MM-PBSA, which is why I need this special
kind of topology file.
Best regards,
Holly

> 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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--
Department of Physics, University of Alberta
Edmonton CANADA

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