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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Received on Fri Apr 18 2008 - 21:13:15 PDT
