Analyzing a PDB containing isolated bases

[claudio]

Dear Dr. Lu and 3DNA users,

My name is Claudio. First of all I would like to thank Dr. Lu for making available the program 3DNA to the community. I have a question related to the use of the program. I need to calculate local base-pair and helical parameters for a nucleobase tetrad I optimized in gas phase starting from crystal coordinates (4 isolated bases). I have a way to convert the coordinates from Gaussian03 format to PDB format. All nucleobase coordinates are in this PDB file except for the coordinates of hydrogen atoms used to saturate the N1 or N9 positions, in other words, the PDB file only contains information about the bases, sugar rings and phosphate groups are not there. I ran the analyze module and, of course, it complained about missing atoms, but calculated the parameters anyway. I have been looking at the formulas in the manual and I think I am using the program correctly, since all I want is the data in the bp_helical.par file. However, I have been using the program for just one day and it would be great if you could tell me if there is something wrong with what I am doing. I would greatly appreciate if you could help me with this.

I look forward to hearing from you soon.
With best wishes,

Claudio

[xiangjun]

Dear Claudio,

Thanks for using 3DNA and your nice words about our work. Actually, as I mentioned in previously replies in this forum, it is the 3DNA users that are driving the further refinement and development of the package. Every user's question provide us a new prospective and opportunity to "Kaizen" (improve/refine) it.

Now back to your question, it is okay to run 3DNA on a nucleic acid structure without backbone atoms. The program "find_pair" will find the pairs and "analyze" will provide a detailed output of strucural parameters. Please have a look of the user's manual. The files "bp_step.par" and "bp_helical.par" are mainly for rebuilding purpose.

It will take time to get familiar with 3DNA and to use it more efficiently. If you have any further questions, please come back to this forum. In case you have some specific problems, you can attach your files and we will look into them.

HTH,

Xiang-Jun

[claudio]

Dear Dr. Lu,

I thank you very much for your help. If I have any other questions I will come back here.

Best wishes,
Claudio