how to minimize DNA built with fiber?

[pqtak]

Hi,
I am wondering how to minimize the BDNA built with fiber. Some bonds are broken and I want to improve the DNA by minimization.

[xiangjun]

Could you be more specific? Which model did you use, and what's the sequence? The fiber models from 3DNA should have standard geometry and proper linkage. I am wondering how it could have broken bonds.

Xiang-Jun

[pqtak]

Hi,
Here what you say in one example:

"Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken). This structure can be easily minimized to obtain a better backbone linkage."

I got some long O3'(i-1) to P(i) bonds and would like to minimize the structure to fix it.

[pqtak]

Hi Xiangjun,
this DNA came from a protein-DNA complex, but the initial parameters were not good. So, I rebuilt it with your program, but before I put it back in the structure of the complex for the refinement, I want to connect all O3'-P linkages. Some distances are >2.5 A.

[pqtak]

By the way, I find that dna residues numbering is not very convenient in the rebuilt dna; chain B continues the numbering from chain A. So, I have to change the numbering manually.