Thanks!
On Sun, Nov 8, 2009 at 3:16 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> There are no scripts in the amber distribution that will do this mutation
> for MM-PBSA to use with alanine scanning. The only way to make this
> mutation is to create a PDB (you can use ambpdb), change GLY to ALA at the
> desired residue (deleting the hydrogens attached to CA) and loading the
> structure into leap. Leap will add the other atoms, but I don't know what
> algorithm it uses to do so.
>
> Good luck,
> Jason
>
> On Sun, Nov 8, 2009 at 2:14 PM, manoj singh <mks.amber.gmail.com> wrote:
>
> > Thanks for your reply.
> >
> > I understand the Gly can attain all PHI and PSI values, however other
> amino
> > acids can not. But, if the Gly is in "usual" conformation, is it possible
> > to
> > mutate it to Ala using any available technique/script in the process of
> > performing MM-PBSA.
> >
> > One more thing, when talking about electrostatic energy, one should not
> > forget desolvation energy.
> >
> > Manoj
> >
> >
> > On Sun, Nov 8, 2009 at 12:53 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > Hello,
> > >
> > > You can write your own script/program to do the transformation. Soon
> > there
> > > will be a release of a new MM-PB(GB)SA script for amber that should be
> > > faster and more user-friendly (and should handle alanine-scanning more
> > > easily). However, even this new script does not handle Gly-Ala
> mutations
> > > since this is more complex than every other mutation. For every other
> > > residue, all that is needed to handle an alanine mutation is to remove
> > > extraneous atoms and readjust some bond lengths to match those in
> > alanine.
> > > Glycine is the only amino acid that has fewer atoms than alanine, so in
> > > order to perform that mutation, atoms would need to be added to the
> > system.
> > > This is non-trivial, because the question becomes "where do we add
> those
> > > extra atoms?" (Ala has more degrees of freedom than Gly)
> > >
> > > It may even be the case that in a specific conformation, an alanine
> would
> > > not even fit where there's a glycine, so you would get an unphysically
> > high
> > > penalty for mutating that residue. Thus, the short version, there is
> no
> > > clear-cut, systematic way to handle a Gly->Ala mutation, so it's not
> > done.
> > >
> > > Furthermore, alanine scanning is designed more to measure the
> > electrostatic
> > > (and perhaps VDW) effects that a particular sidechain has on the
> activity
> > > of
> > > a protein. Glycine (and proline, though Pro->Ala is an allowed
> mutation
> > in
> > > the upcoming version if not this one) more often serves a role in
> > > modulating
> > > the structure of a protein, so alanine scanning is often ill-suited to
> > > probing the importance of a Glycine in the first place.
> > >
> > > Hope this helps,
> > > Jason
> > >
> > > On Sun, Nov 8, 2009 at 12:25 PM, manoj singh <mks.amber.gmail.com>
> > wrote:
> > >
> > > > Hi all!
> > > >
> > > > The mm_pbsa.pl can't do Gly->Ala mutation. Is there any way to do
> this
> > > > mutation in trajectory.
> > > >
> > > > Sincerely,
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > ---------------------------------------
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Nov 08 2009 - 13:30:02 PST
