AMBER Archive (2003)

Subject: Re: AMBER: aminoacid mutation

From: Amber Administration (amber-admin_at_scripps.edu)
Date: Tue Oct 28 2003 - 16:34:47 CST

Hello,

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Amber Admin

---------- Forwarded message ----------
Date: Tue, 28 Oct 2003 12:35:33 -0800 (PST)
From: owner-amber_at_scripps.edu
To: owner-amber_at_scripps.edu

Reply-To: "Carlos Simmerling" <carlos.simmerling_at_stonybrook.edu>
From: "Carlos Simmerling" <carlos_at_csb.sunysb.edu>
To: <amber_at_scripps.edu>
References: <000001c39cf8$7655c1e0$6601a8c0_at_Lauren> <Pine.GSO.4.53.0310281220380.13626_at_marcy.nas.nasa.gov>
Subject: Re: AMBER: aminoacid mutation
Date: Tue, 28 Oct 2003 15:34:44 -0500
Organization: Stony Brook University
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in this case can't you just rename the residue in the
pdb and delete the side chain atoms, letting leap
build it for you? that's what I have done in the past.
you don't get the best conformation, but you at least
get starting coordinates.
Carlos

----- Original Message -----
From: "Ioana Cozmuta" <ioana_at_nas.nasa.gov>
To: <amber_at_scripps.edu>
Sent: Tuesday, October 28, 2003 3:25 PM
Subject: RE: AMBER: aminoacid mutation

> Hi Yong and amber users,
>
> I think I am talking about a much simpler case. What you are referring to
> is how difficult/simple the mutation from an AA to another is from
> energetic point of view (alchemy). I may come to that later as well but at
> the moment the AA I want to mutate is a side chain that points towards the
> inside of a beta-barrel that seems large enough. Actually I want to do a
> couple of mutations: MET to ALA, MET to LEU etc and see how this
> influences the properties of ionic solution inside the beta barrel. I
> think for this purpose a simple geometric modification (preserving the
> position of the alpha Carbon only) with local equilibration of the AA
> should work fine. However any comments on possible issues I should be
> aware of are welcome!
>
> THanks,
> Ioana
>
> On Mon, 27 Oct 2003, Yong Duan wrote:
>
> >
> > Dear Ioana:
> >
> > I am interested in that too. So, let me know if you, or anybody else,
> > know a way or a program to do this automatically.
> >
> > LEU -> ALA mutation is simple. But ALA -> LEU can be a bit tricky if it
> > has to potential to bump into other neighboring atoms.
> >
> > yong
> >
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of Ioana Cozmuta
> > Sent: Monday, October 27, 2003 7:46 PM
> > To: Amber List
> > Subject: AMBER: aminoacid mutation
> >
> >
> > Hi amber users,
> >
> > Is there a way to "automatically" mutate an aminoacid from a protein
> > structure into another one. Say I want to replace an ALA aminoacid with
> > a
> > LEU aminoacid. Is it possible just to select the ALA aminoacid I want to
> > mutate and turn it into LEU? Is there some software out there that
> > could do this on a more automatic basis?
> > The way I thought doing it was to edit the pdb file myself and try to
> > edit
> > the coordinates of the atoms in the new aminoacid such that the bond
> > lengths are preserved and then equilibrate the new positions. But then
> > my
> > boss told me to try "not to lose time with this" and find a software
> > that
> > does it automatically :)
> >
> > Any suggestions are welcomed!
> > Thanks,
> > Ioana
> >
> >
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