Topics

1

General discussions (Q&As) / script for extracting data from 3DNA output file

« on: December 24, 2010, 02:07:40 am »

Dear 3DNA users,
               I am using Amber for MD simulation. I generated hundreds of pdbs from the trajectories and analyzed DNA using 3DNA programe. It will be helpful for  me if someone have a script for extracting information from 3DNA output file. For e.g. I want to extract the twist value for each base pair step of the dodecamer DNA and average it over number of frames.

Thanks in advance

Sincerely
Aneesh

2

General discussions (Q&As) / Methodology for sugar puckering calcualtion

« on: July 23, 2010, 05:30:10 am »

Dear 3DNA users,

                Can anyone tell me what methodology ( mathematics) 3DNA using for calculating sugar puckering in nucleotides ( any reference ) ?.

Thanks in advance

Sincerely
Aneesh

3

General discussions (Q&As) / analysis along the md trajectories

« on: July 21, 2010, 01:26:44 pm »

Dear 3DNA users,

I am using Amber 9.0 for MD simulation of B-DNA. I want to calculate the minor groove width along the 50ns length simulation.Is it possible to do such calculation with 3DNA  without generating snapshots (pdb files) at different time intervals?. Waiting for your valuable reply

Thanks in advance


Sincerely
Aneesh