Messages

1

General discussions (Q&As) / how x3DNA locates the base-pairs for calculating the helical parameters

« on: January 10, 2017, 12:32:59 am »

Dear All,
I wanted to understand how x3DNA locates the base-pairs for calculating the helical parameters from a PDB coordinate file. Specifically, does it find the corresponding base pairs from the same residue number, or, does it find the right base-pair that is spatially closest?
For example, one may have a n-length sequence which is -(AT)- . For, say, the 10th base (A), will it locate the corresponding 10th (T) nucleotide?
How can I interpret it from the generated output file?
Your help is greatly appreciated.

2

MD simulations / Re: x3dna_ensemble analysis error

« on: December 02, 2016, 12:14:32 am »

Hi,

Thank you for pointing out the problem.

It is working now.

Brataraj

3

MD simulations / Re: x3dna_ensemble analysis error

« on: November 30, 2016, 01:24:50 pm »

I actually wrote a code to put MODEL/ENDMDL accordingly. So it was not proper then. Is there is any tool for that to do it precisely according to needs?
thankihg you,
Brataraj

4

MD simulations / Re: x3dna_ensemble analysis error

« on: November 30, 2016, 07:52:54 am »

Hi,

The .bps file is attached here.

thanking you,
Brataraj

5

MD simulations / Re: x3dna_ensemble analysis error

« on: November 29, 2016, 11:21:23 pm »

Hi,
Thanks a lot for replying.
Yes it did worked with the example file provided.
I am attaching my .pdb extracted from the trajectory with this post.
I guess it might help you to point out the problem.
Thanking you,
Brataraj

6

MD simulations / x3dna_ensemble analysis error

« on: November 29, 2016, 08:56:37 am »

Hi everyone,

I just started learning the tool and facing a problem. When I am trying to do ensemble analysis this error is coming

any suggestion for what to do?

nsengupta@localhost:~/bg/DNA_project/100AAD/nxt$ x3dna_ensemble analyze -b tm_AAD_20-25ns.bps -e tm_AAD_20-25ns.pdb
        tm_AAD_20-25ns.pdb: with model numbers <= 0
Process model #0        1 / 9
/home/nsengupta/x3dna-v2.3/lib/miscs.rb:47: warning: Insecure world writable dir /home/nsengupta in PATH, mode 040777
mismatch between base-pair info and model file

thanking you,
brataraj