I would assume that MUTANT_ATOM1 should be the SG atom for CYS when using
mm_pbsa.pl. However, once again, there is no need to specify any of this
atomic information using MMPBSA.py, so I would suggest using MMPBSA.py if
possible since there is less chance of making a mistake with the exact
numbering and atom specification.
-Bill
On Wed, Jun 1, 2011 at 7:42 AM, Guenegou, Guillaume [ORDFR] <
GGUENEGO.its.jnj.com> wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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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 - 05:00:04 PDT
