You will need to use the perl script and do a "stability" calculation with
pairwise decomposition. The python version will not allow differing ligand,
receptor, and complex topology files, and you can't do just a single system.
Good luck!
Jason
On Mon, Jul 19, 2010 at 11:12 AM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> Can I do calculate the interaction energy between connected domains of a
> protein using mmpbsa? Pls noted that as the domains are connected in MD but
> separated (with terminal residues) in mmpbsa.py calculation, the prmtop
> files of the individual domains have different number of atoms when compare
> to those used in MD. What should I do in this case?
>
>
>
> Best regards,
>
>
>
> Cat
>
> > From: askamber23.hotmail.com
> > To: amber.ambermd.org
> > Date: Mon, 19 Jul 2010 16:04:23 +0800
> > Subject: Re: [AMBER] Can I calculate the interaction energy between two
> connected domains of a protein?
> >
> >
> > 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 - 11:00:05 PDT
