Re: [AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations?

From: Bill Miller III <brmilleriii.gmail.com>
Date: Wed, 19 May 2010 23:37:59 -0400

This method should work if you treat the entire protein like the complex and
the receptor, with no ligand. Something like this should go in your .DECOMP
section (with COMPLEX=1, RECEPTOR=0, and LIGAND=0 in the .GENERAL section):

DCTYPE 4 # DCTYPE = 3 could also work here
#
COMREC 1-493
COMLIG 0
COMPRI 60-78 304-310
RECRES 1-493
RECPRI 60-78 304-310
RECMAP 60-78 304-310
LIGRES 0
LIGPRI 0
LIGMAP 0

This defines the entire system to be 493 residues and will print the
pairwise interaction energies for residues 60-78 and 304-310. I didn't know
what residues the auto-inhibition loop was interacting with in domain C, so
I just picked residues 304-310 as an example of the residues in domain C
that you would want to know the interaction energies for. You can substitute
the correct numbers here. In my experience, though, this should give you the
numbers you want for a system that lacks a ligand.

Good luck!

-Bill

2010/5/19 YuZhihong <comfort_79.hotmail.com>

>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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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 - 21:00:04 PDT
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