Analyzing ssDNA

[Orn]

Hi Dr. Lu,

I am trying to compare the structure of my ssDNA to that of standard B- and A-form DNA. I have already generated the .inp file for the analyze command. However, when I ran the script it, I received the following error message "illegal number (<=0) of base-pairs".

Sincerely,
Orn

[xiangjun]

Hi Orn,

Thanks for using 3DNA.

The error message means your ".inp" file does not match your ".pdb" file. Try:
[pre:3dmejz8w]find_pair -s your.pdb stdout[/pre:3dmejz8w]what do you get?

If that does not help solve your puzzle, please provide your ".inp" and ".pdb" files so I can check into the details.

HTH,

Xiang-Jun