Thank you all for your help! Very good suggestions. I am using swiss PDB
right now.
I said 3+ as I could think of at least 1 if not multiple more ways to do it
(other applications or combinations of applications).
On Mon, Sep 10, 2012 at 3:43 PM, Carmenza Martinez <crm3680.gmail.com>wrote:
> sorry I meant to say just as Prof. Simmerling said...the said got
> deleted...sorry
>
> On Mon, Sep 10, 2012 at 3:39 PM, Carmenza Martinez <crm3680.gmail.com
> >wrote:
>
> > 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
> >
> >
>
>
> --
> Carmenza Martinez
> _______________________________________________
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>
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Received on Mon Sep 10 2012 - 14:00:03 PDT
