Just as an addition/question here concerning the LEaP approach: if you
delete everything EXCEPT the backbone AND beta-carbon (or in the case of
mutating glycine to something, just rename the "sidechain" hydrogen to a
carbon) would LEaP then use that and thereby avoid the problem of messing
up chirality or something extreme, and leave you only with the problem or
steric clashes?
If so, it's clearly not as ideal as using a program that has a rotamer
library as has been suggested here, but still isn't devestating if you are
willing to do some minimization or something or the sort.
~Aron
On Mon, Sep 10, 2012 at 4:30 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> 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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> > >> > AMBER.ambermd.org
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> > >> >
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> > >>
> > >
> > >
> > >
> > > --
> > > Carmenza Martinez
> > >
> > >
> >
> >
> > --
> > Carmenza Martinez
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Sep 10 2012 - 15:00:03 PDT
