Messages

1

MD simulations / Re: Analysis of helical parameter of DNA with unnatural

« on: March 01, 2019, 03:28:43 am »

Dear Xiang-Jun

Web 3DNA 2.0 server at http://web.x3dna.org is not been updated to latest version. Now it is running in 3DNA v2.4.1-2019feb11.

Thanks and Regards
Priyabrata Das

2

MD simulations / Re: Analysis of helical parameter of DNA with unnatural

« on: February 28, 2019, 01:19:07 am »

Dear Xiang-Jun,
 Thank you very much for your previous follow up.

One more query I have, when I am running my attached PDB file it shows only 13 base pairs instead of 16 base pairs.
For your reference, I had attached the output file. Kindly suggest, how to find the parameter for all 16 base pair.

Thanks and Regards
Priyabrata Das

3

MD simulations / Re: Analysis of helical parameter of DNA with unnatural

« on: February 26, 2019, 11:56:24 pm »

Dear Xiang-Jun,

Thank you very much for your follow up.


Thanks and Regard
Priyabrata Das

4

MD simulations / Analysis of helical parameter of DNA with unnatural

« on: February 18, 2019, 06:09:48 am »

We are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, the base pair  DX:DY was not be recognized when I used “find_pair”. Notably, the unrecognized base-pair ( DX, DY ) are not typical purine or pyrimidine. How can I analysis the confirmation parameters with 3DNA in such case? 

  The PDB files of DX, DY,  and a frame of MD simulations(XY.pdb) are given in the attachment. Thank you very much!

Thanks and Best wishes

Priyabrata Das