unanswered Martnini-nucleotide.py add constraints to backbone or manual

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4 years 4 months ago - 4 years 4 months ago #8334 by daniloboskovic
Dear caretakers/experts,

I am in dire need of help regarding nucleic acid backbone constraints. Namely i need to put several nucleic acids in a constrained position during energy minimization to prevent it from dissociating. I do understand there is a constraints section in the ITP file that has the following format:

[ constraints ]
3 4 1 0.29600 ; G
4 5 1 0.29100 ; G
5 6 1 0.29600 ; G
6 3 1 0.16200 ; G

as well as a backbone bonds section:

[ bonds ]
; Backbone bonds
1 2 1 0.20200 40000 ; G(C)-G(C)
2 7 1 0.35400 10000 ; G(C)-G(C)
7 8 1 0.36300 20000 ; G(C)-G(C)

Now i can do it manually by adding entries in the constraints section from the backbone section (and calculate value example 1 2 1 x.xxxxx ; G(C)-G(C))

or

edit the script. In the script there is a comment that one can add backbone constraints.

So my question is how do i calculate x.xxxxx for these bonds or how do i edit the script to include backbone constraints?

Thanks!
Last edit: 4 years 4 months ago by daniloboskovic.

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