Hello,
My best advice would be to use MM/PB(GB)SA decomposition analysis. If you
use pairwise decomp and you're clever about it, you can work your way back
to the quantity you're looking for.
Good luck!
Jason
On Mon, Jul 19, 2010 at 4:04 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Thank you,
>
>
>
> Thanks for your help. However, when I divide the two domains into two pdb
> file, the xleap will add terminal residues to each domains. Let's the
> following example
>
>
>
> For the orginal protein, that I run the MD, I should have following
> sequence for the protein
>
>
>
> C-terminal-domain1-domain2-N-terminal
>
>
>
> However, if I just separate two domain in pdb file, and prepare prmtop from
> there, I will have
>
>
>
> C-terminal-domain1-N-terminal AND C-terminal-domain2-N-terminal
>
>
>
> As the number of atoms no longer match the MD trajectory, I will not be
> able to get the binding energy correctly. That's why I would like to ask
> for additional advices for AMBER's users or experts. Is there any way to
> estimate the interaction energy between domain 1 and domain 2 using AMBER?
>
>
>
> best regards,
>
> cat with thanks.
>
>
>
>
>
> > Date: Mon, 19 Jul 2010 09:45:08 +0200
> > From: rubben.torella.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Can I calculate the interaction energy between two
> connected domains of a protein?
> >
> > In order to obtain the prmtopof the two domains, I guess you could
> "divide
> > the domain" with Pymol or VMD, and save two pdb, one for each domain.
> Then
> > with different pdb you can build two different prmtop.
> > I hope this works.
> > Bye
> >
> > 2010/7/19 Catein Catherine <askamber23.hotmail.com>
> >
> > >
> > > Dear Sir/Madam,
> > >
> > >
> > >
> > > I am trying to calculate the interaction energy between domain 1 and 2
> of a
> > > protein. Since domain 1 and 2 are connected, i cannot define a
> separated
> > > prmtop file for each domain. I guess I cannot use MMPBSA/GBSA methods
> to
> > > get this interaction energy. Are there any other methods I can use to
> > > estimate the binding energy between domains?
> > >
> > >
> > >
> > > Best regards,
> > >
> > >
> > >
> > > Cat with thanks.
> > >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 19 2010 - 08:30:04 PDT
