Messages

1

MD simulations / Analysis of major groove and minor groove

« on: November 20, 2017, 11:36:51 am »

Hi

About the analysis of major groove and minor groove , in this website ,
http://do-x3dna.readthedocs.io/en/latest/dna_class_api.html#dnaMD.dnaMD.DNA.set_major_minor_groove ,
it said that "The major and minor grooves (direct P-P) cannot be calculated for first and last two base-steps" .

Does any one know the reason why major and minor grooves cannot be calculated for first and last two base-steps ?


Thanks a lot

2

MD simulations / about "curavture" and "tangent" in dnaMD

« on: November 08, 2017, 11:14:05 am »

Hello,

I have a question about the unit of "curavture" and "tangent" in dnaMD. 

In dnaMD, my dna contains 24bp, and I type " dnaMD vsTime -i 24bp_dna.h5 -tbp 24 -bs 1 -be 24 -p "curvature" -mm sum -o curvature.dat ".

An error occur, "The requested end bp 24 is out side of 1-23 range" , why the range is 1-23?

This error occur on "tangent" ,too.

Also,I concern the unit of "curavture" and "tangent" ?



Thank you very much for your help,
Anderson