AMBER Archive (2007)

Subject: Re: AMBER: Problem with calcpka.pl and constant pH

From: David A. Case (case_at_scripps.edu)
Date: Thu May 03 2007 - 12:13:50 CDT

On Mon, Apr 30, 2007, Hayden Eastwood wrote:
>
> My output contains no reference to the numerous ARG residues that exist in
> the protein sequence - is this because ARG is not supported as a residue
> within the constph algorithm?

That is correct: see the package CPinData section of CPin.pm (in your
executable directory). The needed charge changes (on going from protonated to
neutral ARG) would need to be added there.

...regards...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu