Dear Cat,
You could try using sietraj (
http://www2.bri.nrc.ca/ccb/pub/sietraj_main.php). This allows you to define the atoms considered as "target" and "ligand" even if the system is one chain. However, to avoid extreme "nonbonded" interactions between atoms that are actually bonded you should leave out one residue between the domains when defining the target and ligand sets. (Note that you do not have to actually delete the residue; just don't include it in the set definition.) Also, to reduce solvation artifacts, it would be good to zero the partial charges of the residue you are leaving out of the set definitions. Hope this works for you.
Enrico
-----Original Message-----
From: Catein Catherine [mailto:askamber23.hotmail.com]
Sent: Monday, July 19, 2010 4:04 AM
To: amber.ambermd.org
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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Received on Mon Jul 19 2010 - 09:00:03 PDT
