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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>>
>
>
>
> --
> 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 - 06:30:05 PDT
