Yikes, point taken.
Also for anyone who finds this thread, PyMol has a mutation function that
uses a rotamer library.
~Aron
On Mon, Sep 10, 2012 at 6:24 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> what often happens in my experience is that the steric clashes are bad
> enough that the atoms get pushed around, and the chirality inverts because
> of that. eventually you minimize the clash away, but in the process things
> are no longer correct. we've even seen really weird cases such as where a
> Phe ended up with a protein chain going through the middle of the ring-
> obviously no way that will ever get fixed in MD.
>
> I guess I'm just warning people that if you have a high energy structure,
> just because you minimize it doesn't mean things are ok. you should always
> visually inspect the area where you made the change.
>
>
> On Mon, Sep 10, 2012 at 5:53 PM, Aron Broom <broomsday.gmail.com> wrote:
>
> > 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.
> > > > >> >
> > > > >> >
> > > > >> >
> > > > >> > _______________________________________________
> > > > >> > AMBER mailing list
> > > > >> > AMBER.ambermd.org
> > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> >
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
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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
> > _______________________________________________
> > 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 - 18:00:03 PDT
