Sorry, I did not precise I use mm_pbsa.pl with amber11.
So I have to write atom numbers in the input file.
The question could be: the MUTANT_ATOM1 has to be SG for CYS (as OG for
SER)?
-----Original Message-----
From: Bill Miller III [mailto:brmilleriii.gmail.com]
Sent: mercredi 1 juin 2011 12:48
To: AMBER Mailing List
Subject: Re: [AMBER] Alanine scanning with CYS
I believe it should work with both mm_pbsa.pl and MMPBSA.py, but I know
that
it will work with MMPBSA.py. And with MMPBSA.py, you do not need to
specify
any pointer atoms in the input file. MMPBSA.py will determine which
residue
you want mutated based on the provided prmtop files, so there is really
no
atom information you need to provide about the mutated residue.
I hope that helps.
-Bill
On Wed, Jun 1, 2011 at 4:53 AM, Guenegou, Guillaume [ORDFR] <
GGUENEGO.its.jnj.com> wrote:
> Dear all,
>
> I would like to run trials with alanine scanning. I understand why
there
> are special cases. But I do not understand why there is no precision
> about CYS in documentation whereas SER (similar to CYS) is treated.
> Do I have to make an extrapolation for CYS? Or its case is not
treated?
>
> Thanks for any answers,
> G.GUENEGOU
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Jun 01 2011 - 05:00:02 PDT
