Hi, Bill
Thanks for your suggestions! Yes, there is only one true molecule with A,B and C domains in my simulations. I've tried as you said, but it looks like I must set the residue numbers for all COM*, REC* and LIG* in the .DECOMP section, even I set RECEPTOR and LIGAND to 0 in the .GENERAL, otherwise the mm_pbsa.pl will not work. My protein has 493 residues, the auto-inhibition loop is from 60 to 78, then do you think what numbers I should set for COM*, REC* and LIG* in the .DECOMP? I have tried many numbers, but all of them were failed.
Zhihong
> Date: Tue, 18 May 2010 20:05:59 -0400
> Subject: Re: [AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations?
> From: brmilleriii.gmail.com
> To: amber.ambermd.org
>
> If I understand your question correctly, there is only one true molecule
> with three different domains, thus the idea of 'ligand' and 'receptor' is
> not really applicable in your case. However, you can do a calculation with
> mm_pbsa.pl in which you only perform a calculation on a complex (setting
> COMPLEX equal to 1, and RECEPTOR and LIGAND to 0 in the general section).
> Then you can choose to do a pairwise per-residue decomposition calculation
> (setting DC to 1 and DCTYPE equal to 3 or 4). This will give you the
> interaction energy for each residue in the complex interacting with every
> other residue in the complex. Furthermore, you can choose to only print a
> subset of the residues in the complex (i.e. only the residues in the loop of
> domain A and few residues in domain C you are concerned with) by specifying
> those residues with the variable COMPRI in the .DECOMP section.
>
> I hope that answers your question(s). Good luck!
>
> -Bill
>
> 2010/5/18 YuZhihong <comfort_79.hotmail.com>
>
> >
> > Dear AMBER users,
> >
> > Now I'm studying a protein by MD simulations, this protein have three
> > domains of A, B and C, one loop in A (call auto-inhibition-loop, AIL)
> > interacted with a few residues in C and formed a so-called “auto-inhibition”
> > state. I introduce a mutation at one interacting site in C and have finished
> > 20ns MD simulations for both wild-type and mutant. Now I want to get the
> > interaction energy of AIL with those residues in domain C from both MD
> > trajectories, here is some questions:
> >
> > 1). Can I achieve the objective based on already finished classical MD
> > simulations through some post-process, such as MM_PBSA/GBSA?
> >
> > 2). If I can get this type of interaction energy through MM_PBSA/GBSA, then
> > how will I set input values in mm_pbsa.in, especially for
> > COMPT/RECPT/LIGPT in .GENERAL section, and corresponding residue numbers in
> > .DECOMP section? Supposing the organization of this protein is like:
> > Domain A: 1 ~ 100
> > AIL: 60 ~ 70
> > Domain B: 101 ~ 200
> > Domain C: 201 ~ 600
> >
> > 3). To get the total interaction energy of AIL with nearby residues in
> > domain C, which type of energy decomposition is better for summing up,
> > per-residue or pairwise per-residue? Which value is the best for DCTYPE?
> >
> > 4). If I can’t get this interaction energy based on finished MD
> > simulations, can I get it by running other MD simulations in Amber9? Then
> > which key parameters should I modify?
> >
> > 5). Even if the answer of 4) is “No”, could you give me some suggestions on
> > how to compare the “binding affinity” of AIL to domain C in wild-type and
> > mutant through computational technique?
> >
> > Thanks in advance, and I really, greatly appreciate any advice!
> >
> >
> >
> >
> >
> > Zhihong
> >
> > _________________________________________________________________
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> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Wed May 19 2010 - 09:30:04 PDT
