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Questions and answers => General discussions (Q&As) => Topic started by: Orn on August 19, 2011, 12:32:50 pm

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Title: Analyzing ssDNA
Post by: Orn on August 19, 2011, 12:32:50 pm

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

Title: Re: Analyzing ssDNA
Post by: xiangjun on August 19, 2011, 09:08:53 pm

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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University