the sign of minor or major groove width

[shahabshariati]

Dear all

I did MD simulation of DNA by amber. Then I obtained minor or major groove width by cur+ and canal.

in output relating to minor or major groove width, there are number with negative sign. can width values be negative?
are my output file wrong? if so, how to fix it?

is there problem in cur+ and canal program.

If I obtain above parameters with 3DNA, there isn't same problem. is it true?

please guide me.

best regards

[xiangjun]

3DNA calculates minor and major groove widths, following El Hassan and Calladine:

[pre:4yesx38r]Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of                          
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.[/pre:4yesx38r]
By definition, the groove widths output from 3DNA should be positive.

HTH,

Xiang-Jun

[shahabshariati]

Dear xiangjun

thanks for your reply.

I want to know there is this possible that groove widths be negative. My mean is in experiment and not in the output from 3DNA or curve.

best regards.

[xiangjun]

Well, I can only help with 3DNA. As I said in my previous post, all groove dimensions from 3DNA are positive.

To be specific with any further discussion on this thread, please provide a PDB file (possibly with a picture as well) which has "negative" groove width.

HTH,

Xiang-Jun