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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Received on Mon Jul 19 2010 - 01:30:03 PDT
