Topics

1

MD simulations / issues with x3dna_ensemble

« on: May 30, 2013, 10:48:32 am »

Hi  all,,
I need some help. I am trying to use x3dna_ensemble to calculate the inter-base step parameters. I am trying to follow the steps mentioned by Xiang-Jun in the following post: http://forum.x3dna.org/md-simulations/how-to-properly-use-x3dna_ensemble/
this is what I did so far
1. I went inside the directory,
     X3DNA/x3dna-v2.1beta/examples/ensemble/md
2. Issued the command
     x3dna_ensemble analyze -h
but it is giving me the following message:
/usr/bin/env: ruby: No such file or directory
I also tried typing:
~/X3DNA/x3dna-v2.1beta/bin/x3dna_ensemble analyze -h
still got same message

In my .bashrc file, I have included the following two lines when I first installed (few months ago) x3DNA
export X3DNA=/home/shyno/X3DNA/x3dna-v2.1beta
export PATH=$PATH:$X3DNA/bin

thanks,
Shyno

2

MD simulations / analyzing longer DNA sequences

« on: November 20, 2012, 02:01:37 pm »

Hi all,

I am having difficulties analyzing a 62 base pair long DNA.I am using find_pair along with Curves+.
The 3DNA version I use -x3dna-v2.1beta
What is the default number of base pairs find_pair can analyze? Is there a way to increase this value?

Thanks
Shyno

3

MD simulations / pdb files created using v 1.5 and v 2.1 beta

« on: May 29, 2012, 06:12:12 pm »

Dear users,

Initially I was using X3DNA v 1.5 for creating a pdb file, which I used for studying mutations.
Only recently I realized there are new versions of X3DNA and I tried creating the same pdb file using v 2.1 beta.
These two files seems to be different. Can anyone comment on this? does it mean the pdb file I created using v1.5 is not good?

Thank you very much,
Shyno Mathew

4

MD simulations / No matching entry in atomlist.dat

« on: April 29, 2012, 07:49:24 pm »

Dear all,

I am trying to use find_pair as shown below:
find_pair -c+ sel.pdb new.inp
I am getting this error: no matching entry for atom name [  OW] (..OW) in 'atomlist.dat'
   now it is set as 'XX'
In my pdb file water is listed as OW. In this case should I add this as a new atom to atomlist.dat?
For the same analysis, I had to modify baselist.dat. The following bases were added:
DG3- 3 terminal guanine
DC5- 5 terminal cytosine

thanks
Shyno