For alanine scanning, only the mdcrd file for the wild-type is needed
because the coordinates from the wild-type trajectory are "mutated" to the
alanine mutant and used for the mutant trajectory instead of the user
running a completely separate MD. This is intended to save the user the
computational time of running another MD. Of course, this is an
approximation and any conformational (local or global) changes that would
arise from the mutation would not be captured using this method.
Theoretically, it should be more accurate to run two independent MD runs for
the wild-type and the alanine mutant, since this would capture more of the
effects associated with the mutation.
I hope that helps.
-Bill
On Fri, Apr 1, 2011 at 4:15 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Hi Amber users,
> I read through the tutorial concerning binding energy calculations for
> the
> wild type and alanine mutant (alanine scanning). What I understand from
> the
> tutorial is that the mdcrd file is needed only for the wild but not for
> the
> mutant (which means we do not need to run MD simulation for the mutant),
> am
> I right???
> My second question is, if I run two independent MD runs for the wild and
> the
> alanine mutant, then calculate the PBSA binding energies for these two
> systems independently, will that give me more accurate estimate about the
> contribution of alanine to the binding than the scanning procedure does?
> Best wishes
> Mahmoud
> _______________________________________________
> 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
Received on Sat Apr 02 2011 - 08:00:04 PDT
