---------- Forwarded message ----------
From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 24 Dec 2013 13:57:55 -0500
Subject: Re: [AMBER] doubt in alanine scanning of phosphorylated residue
To: suma jayakrishnan <sumajayakrishnan.jk.gmail.com>, AMBER Mailing
List <amber.ambermd.org>
Please keep these messages on the Amber mailing list. Also, the code that
I mainly work on now is from AmberTools 13, so it would be best to upgrade
to that version. That said, the alanine scanning code has been largely
unchanged since the original release several years ago, so my advice may
still apply to your version.
On Tue, Dec 24, 2013 at 12:09 AM, suma jayakrishnan <
sumajayakrishnan.jk.gmail.com> wrote:
>
>
> Dear Jason,
>
>
> Thank you for your reply.
>
>
> I was trying to mutate the phosphorylated serine S2P to ALA. and the error
> was
>
>
>
>
>
> "Error: Unrecognized residue. Add S2P to getnumatms(resname)."
>
>
>
>
>
>
>
>
>
> So i included getnumatms, getressymbol definitions as 14 and X in
>
>
> utils.py.
>
I don't think anything needs to be added to utils.py (just alamdcrd.py).
You need to modify _getnumatms to specify the number of atoms in the S2P
residue and you have to modify the _mutate functions in alamdcrd.py, adding
S2P to one of the lists. I believe in listone, the mutation begins at the
7th atom (and for listtwo it begins at the 6th atom and listthree
special-cases proline, which is quite different).
I cannot recall off the top of my head exactly how alamdcrd.py performs the
mutations, so you will have to compare the existing amino acid residues (in
the amino acid library files in $AMBERHOME/dat/leap/lib) with your residue
to see how their treatment differs.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 24 2013 - 19:00:08 PST
