Messages

1

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

« on: January 12, 2011, 12:31:47 am »

Dear Alpay and Xiang-Jun,
                     Thanks for your reply. I will definitely go through the suggestions you made and will update you about it.

Thanks once again

Sincerely
Aneesh

2

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

« on: January 07, 2011, 04:18:58 am »

Dear Xiang-Jun,
             I can convert each snapshots into  PDBs. All the PDBs are stored in the same directory and all of them share a specific pattern of names, like 3dna_1.pdb, 3dna_2.pdb etc.

            Is there any other way in your mind to analyze the large number of 3DNA ouptuts generated for MD trajectories?

Sincerely
Aneesh

3

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

« on: January 06, 2011, 04:17:39 am »

Thanks for the immediate reply.

>Are the 100 snapshots stored in 100 separate PDB files, or all in one?
           They are stored in 100 seperate PDBs.
> What would be an appropriate output format for the extracted parameters?
       For e.g. Below is the part of 3DNA output file.
****************************************************************************
Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 CG/CG     -0.47      0.25      2.95     -3.89      5.88     26.83
   2 GC/GC     -0.38      1.12      3.63     -1.47    -11.72     51.06
   3 CG/CG     -0.59     -0.23      3.19     -6.17      9.46     22.37
   4 GA/TC      1.02     -0.13      3.56      4.26     16.61     29.18
   5 AA/TT     -1.86      0.42      3.30     -0.02      1.06     40.25
   6 AT/AT      0.09     -0.55      3.44     -9.90     -5.12     33.95
   7 TT/AA     -0.04     -1.23      3.62     -5.80      3.39     34.13
   8 TC/GA     -0.79     -1.74      3.13      3.33     -7.64     31.44
   9 CG/CG      1.87      0.46      3.57      3.93     15.07     30.64
  10 GC/GC     -0.98      0.47      3.21     -6.57     -5.86     40.09
  11 CG/CG      1.38     -0.30      2.83      4.67      1.96     33.37
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.     -0.07     -0.13      3.31     -1.60      2.10     33.94
      s.d.      1.10      0.82      0.28      5.18      9.23      7.71
****************************************************************************
        Here, I want to extract a certain parameter, say Twist, for each base pair step . So the output file contains a single column with twist value  corresponding  to one particular base pair step ( say for 4th step, GA/TC) for which Twist values are  extracted from 100 3DNA outputs ( i.e a single column with 100 lines). This should repeat for all the base pair steps ( I dont have a better idea to do this)  
 

> In addition to the mean values of some parameters, e.g., Twist, how about their standard deviations and other related simple statistics?

     At the end of the column contains the mean value and standard deviation for that particular base pair step.


Hope this will help

Sincerely
Aneesh

4

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

« on: January 04, 2011, 12:51:40 am »

Dear Dr. Xiang-Jun,

           Thanks for the reply. In my case, I am using a dodecamer B-DNA and  have generated 100 snapshots (PDBs) from the simulation trajectories. Followed by this I have done the 3DNA analysis for each snapshot and  got 100 3DNA output files. Now I want to extract different parameters from the output file. For e.g, I want to get the  average 'Twist' value for each base pair step. For that I have to extract Twist value for each base pair from 100 3DNA output files and average it and calculate the standard error.

Hope I made it clear now.

Waiting for your valuable reply.

Thanks in advance

Sincerely
Aneesh

5

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

6

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

« on: July 24, 2010, 01:34:49 am »

Dear Dr. Xiang-Jun,

Thanks for your quick reply


regards
Aneesh

7

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

8

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

« on: July 22, 2010, 01:42:42 am »

Dear Dr. Xiang-Jun,

Thank you for the immediate reply.


Regards
Aneesh

9

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