Messages

1

General discussions (Q&As) / Re: Analyzing a PDB containing isolated bases

« on: November 16, 2006, 07:28:08 am »

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

2

General discussions (Q&As) / Analyzing a PDB containing isolated bases

« on: November 15, 2006, 09:15:28 am »

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