You will need both a mutant complex and a mutant receptor topology files for
each mutation. So to make two different mutations, you will need to create
four new topology files. The coordinate files are unnecessary for MMPBSA.py.
I hope that answers your question.
-Bill
On Tue, Apr 26, 2011 at 9:26 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Bill
>
> Many thanks for your help. I'd appreciate one additional clarification
> please:
>
> You write " mm_pbsa.pl can mutate more than one residue to alanine at a
> time. MMPBSA.py
> will need to perform different calculations for each mutation"
>
> Assuming that I need to mutate two residues, do I need to generate 2
> coordinate and 2 topology files (one for each mutation) and then run
> MMPBSA.py for each mutant?
>
> All the best
>
> George
>
> On Apr 26, 2011, at 2:59 PM, Bill Miller III wrote:
>
> > See comments below.
> >
> > -Bill
> >
> > On Tue, Apr 26, 2011 at 8:50 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> I'd appreciate any feedback on the following two questions:
> >>
> >> 1. Can one mutate more than one residue to alanine(s)?
> >>
> >
> > mm_pbsa.pl can mutate more than one residue to alanine at a time.
> MMPBSA.py
> > will need to perform different calculations for each mutation.
> >
> >
> >>
> >> 2. Is it really essential that the pdb and topology files of the mutant
> be
> >> created prior to running the simulations? The reason I'm asking this is
> to
> >> ascertain whether one will have to re-run previous equilibration and
> >> production simulations.
> >>
> >
> > When doing alanine scanning with MM-PBSA inside Amber the coordinates
> from
> > the original trajectory are simply modified to accommodate an alanine
> > residue instead of the original residue. No additional simulations are
> > performed by MM-PBSA. The reasoning behind making the pdb and topology
> files
> > prior to running the simulation is for consistency sake. In other words,
> > this is a suggested note to help the user be consistent in case prep
> files
> > are lost or deleted accidentally during the simulation.
> >
> >
> >>
> >> Many thanks in advance for your help
> >>
> >> George
> >>
> >> _______________________________________________
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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
> > _______________________________________________
> > 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 Tue Apr 26 2011 - 07:00:02 PDT
