Messages

1

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 16, 2012, 11:13:36 am »

Dear Dr. Lu,

It seems that everything is fine. Thank you very much.

All the best,
Ali

2

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 13, 2012, 02:09:22 pm »

Thank you for your reply. I mean geometric center of ring atoms.

3

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 13, 2012, 10:24:53 am »

Hi Xiang-Jun,

My DNA stretching simulations result in conformations in which some interstrand base stackings can be seen (please see attached snapshot). To determine the interstrand base stacking or temporary itrastrand base stacking interaction made in non-canonical conformation of double stranded DNA, I think information about position of center of bases on each strand and their normal vector are needed.  Could you please add such information to the outputs of 3DNA?

Thank you,
Ali

4

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 11, 2012, 03:49:20 am »

Thank you very much for your responses and your good software.

Best wishes,
Ali

5

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 10, 2012, 04:13:41 am »

Hi Xiang-Jun,

Thank you for your update ans suggestion. I encountered a problem with new release of 3DNA at the first step, i.e. when I used “find_pair”. When I tried

>> find_pair actg3_md.pdb bpfile.dat

I got errors such as follows

-----
no matching entry for atom name [] (...) in 'atomlist.dat'
   now it is set as 'XX'
   check and update file $X3DNA/config/atomlist.dat
-----

actg3_md.pdb is a PDB MODEL/ENDMDL ensemble created by AmberTool12 (the PDB file is attached). By the previous release (2012Nov26) there is not any problem!
When I used bpfile.dat (created by the previous release of 3DNA) with “x3dna_ensemble” of the current release to see the changes you added (>> x3dna_ensemble analyze -b bpfile.dat -e actg3_md.pdb -o ensemble.out), I got the following error:

-----
mismatch between base-pair info and model file
-----

Would please help me? The bpfile.dat file is attached too.
Is it not possible that 3DNA analyze directly the output trajectory file of famous MD codes such as Amber?

With best regards,
Ali

6

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 09, 2012, 04:16:08 am »

Hi Xiang-Jun,

Thank you very much for your reply. The problem is exactly what you understand. In fact, I want to calculate the number of inter- and intrastrand base stacking for a DNA under stretch. My calculations uses a geometrical criterion that two bases are stacked when the distance between the centers of the rings is <0.45 nm, and the angle between the normals to the bases is <30 degree (based on the information obtained by 3DNA for the origin and mean normal vector of each base-pair). Then, I will plot the variations of number of base stackings as a function DNA length (or simulation time). I hope these explanations are sufficient.

Thanks,
Ali

7

MD simulations / Base stacking from x3dna_ensemble

« on: December 08, 2012, 12:46:36 pm »

Dear Dr. Lu,

I used x3dna_ensemble Ruby script to obtain base stacking information from a PDB MODEL/ENDMDL ensemble (for B-DNA conformation). Although the temp_model.out have information about origin and mean normal vector of each base-pair, but unfortunately the ensemble output does not contain such information. Could you please provide me a solution for this problem?

Many thank,
Ali