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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>
--
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 - 06:00:03 PDT
