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.scripps.edu [mailto:owner-amber.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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Received on Tue Oct 28 2003 - 20:53:01 PST
