Topics

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 / 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