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
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > Carmenza Martinez
> > > >
> > > >
> > >
> > >
> > > --
> > > Carmenza Martinez
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Mon Sep 10 2012 - 15:30:02 PDT
