[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

[Justin Lemkul]

On 8/19/19 9:17 AM, sunyeping wrote:
> Hi, Justin:
>
> This is my circumstance: I have a crystal structure of a DNA-binding 
> protein (I call it as "A"), but I cannot get the crystal structure of 
> the A-DNA complex and I have to give a prediction of what the cystal 
> structure of A-DNA complex might be like. So I docked a DNA structure 
> to the crystal structure of A and used the resulting complex as the 
> initial structure for MD simulation and got a trajectory. Now I want 
> to exact the one frame from the trajectory which is most possibly 
> close to the the cystal structure of the A-DNA complex from the 
> trajectory.
>
> Now I have a crystal structure of DNA in complex with a protein (I 
> call it as "B") belonging to the same family as the protein I am 
> studying. So I want to use this available crystal structure of B-DNA 
> complex as a reference structure and find a frame which has the 
> smallest rmsd against B-DNA complex. The problem is, A-DNA and B-DNA 
> have different number of atoms, so gmx rmsd doesn't work. What could I 
> do in such a circumstance?
>

Save a subset of atoms (trajectory and matching .tpr) that are common to 
both and compute the RMSD. That's the only way to do it.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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