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 Tue May 18 2010 - 17:30:03 PDT
