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Messages - arnab

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1
General discussions (Q&As) / Re: A-DNA definition
« on: April 02, 2012, 02:00:40 pm »
Dear Xiang-Jun,

  I will get back to you after checking the steps you suggested. However, what I really meant is to supply the coordinate directly from xtc to 3DNA directly bypassing the pdb so that the analysis is extremely fast. I have done the same with curves (in house) since the source code is available.

  However, this can be done also by generating pdb trajectories at the cost of disk space and slight speed compromise.

Best regards
Arnab

2
General discussions (Q&As) / Re: A-DNA definition
« on: April 02, 2012, 12:38:07 am »
Dear Xiang-Jun,

  Thank you again for clearing the doubt which I was carrying for some time. Wish I could contact you earlier.

  I have a request regarding future implementation of 3DNA. In order to facilitate faster analysis of DNA structures along a MD trajectory, if you could modify slightly to read a trajectory, it will be very useful. Earlier CURVES now changed as CURVES+ can read a trajectory. Right now, I convert my GROMACS trajectory to pdb, then send out for 3DNA analysis and then parse information using a script and this takes time if the trajectory is tens to hundreds of nanoseconds.

 If you don't have time and need additional pair of hands, I can create a patch between GROMACS and 3DNA where a GROMACS trajectory can be analyzed for all 3DNA related information.

 Best regards
Arnab

3
General discussions (Q&As) / Re: A-DNA definition
« on: April 01, 2012, 03:24:08 pm »
To add to my previous post,  the sanity check clears out str221.pdb for 6CG/CG step which has Zp 1.93 but unassigned type. However, I don't know the check corresponding to "WC_info && WC_info[i + 1]  /* WC geometry */". Therefore, this may be a part of the issue of not getting the right form.

4
General discussions (Q&As) / Re: A-DNA definition
« on: April 01, 2012, 03:02:47 pm »
Dear Xiang-Jun,

  As usual, you are extremely prompt and precise in your answer. Your answer and the code snippet clearly explained the definition. However, my doubt arose from my own observation which is explained in detail below.

  During the perturbation to B-DNA, I observed higher Zp of 1.93 (str221.pdb attached) for step 6CG/CG (3DNA output attached as str221.out) . However, this step has not been assigned to A type.

 In comparison some other structures observed 5ps later (str226.pdb and str226.out) was assigned A-form for the same step mentioned above which has Zp=2.09.

 Therefore, I assume there must be more to the story. I will appreciate your help in solving this puzzle.

 Thanks again.

Best regards
Arnab

5
General discussions (Q&As) / A-DNA definition
« on: March 31, 2012, 03:12:48 pm »
Dear Lu and Members,

 What is the exact definition (set of parameters and ranges) used by 3DNA to define a base pair step as A-form, B-form or *TA* form? If it has been discussed already, I will be happy to know the location etc.

Thank you.

Arnab Mukherjee
IISER, Pune

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.