Not sure if anybody has suggested it previously but for single point
mutations or multiple mutations of residues I have found swissPDB to be
quite useful:
http://spdbv.vital-it.ch/
Just as Prof. Simmerling leap is not efficient at filling in the blanks
when you remove things and renamed them just as Francois suggested.
Now, when you say 3+???? I don't understand what you mean...changing the
protonation state perhaps? for that you will need more than what swiss PDB
could provide. Perhaps somebody else in the forum will provide useful
advide for that
Best regards
On Mon, Sep 10, 2012 at 3:01 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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.
> >
> >
> >
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> >
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Carmenza Martinez
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Received on Mon Sep 10 2012 - 13:00:03 PDT
