This isn't a good method- leap doesn't care at all where it puts the side
chain and unless you're very lucky you will have bad steric clashes that
can invert chivalry and other bad things. You want to use a program that
searches rotamers for something that fits as best as possible.
On Sep 10, 2012 2:48 PM, "FyD" <fyd.q4md-forcefieldtools.org> wrote:
> Dear Jonathan,
>
> You could edit the PDB file: (i) remove the side chain of the amino
> acid to be mutated; (ii) rename the backbone of this residue according
> to the residue name of the mutation. Then, you load the modified PDB
> file in the LEAP program, which will automatically add the missing
> atoms (i.e. the side chain) in agreement with the FF library of the
> mutated residue.
>
> regards, Francois
>
>
> > The basic (or complex) question I have is:
> >
> > How do you take a PDB and change one residue to another residue?
> > (essentially a point mutation of an existing structure)
> >
> > I thought I remembered reading how it could be done, but looking back I
> > can't seem to find where it might be. I can think of a few ways one
> could
> > accomplish this, but I wanted to ask if there is an explanation in the
> > manual or a tutorial that I am just missing. (Can someone point me in
> the
> > right direction)
> >
> > 1. I searched the archives and saw some old posts regarding using other
> > programs.
> > 2. One could manually add/change things
> > 3+????
> >
> > Not necessarily looking for a step by step but a push in the right
> > direction.
>
>
>
> _______________________________________________
> 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
Received on Mon Sep 10 2012 - 12:30:03 PDT
