Use of Ensemble function

[clarkt]

Hello,

So I am trying to use x3dna_ensemble analyze and have a folder with multiple .pdb structures.  Whenever this command
is run the error message beneath it pops up

x3dna_ensemble analyze -b bp_order.dat -p 'HJH/100*.pdb' -o 100mM_ensemble.out

Not a duplex: <1>

what does this mean and how to fix it? The pdb structures were generated from a single pdb with multiple frames in VMD and bp_order.dat was the output from the find_pair function.

Thanks,
-Clark

[xiangjun]

Hi,

Without a reproducible example, it's hard to pinpoint where the problem is. From the error message, I'd guess the first structure in your list is not a duplex. Note that 3DNA v2.3 is open source. You may check the Ruby (and C) code for a deep understanding of how x3dna_ensemble works.

Searching the Forum may also help. See the thread "x3dna_ensemble is not working for hairpin loop structures"

Xiang-Jun

[clarkt]

Thank you Dr. Xianjun,
It appears to be working now.  The issue was that bp_order.dat was not the file that I needed to be using.  I had to use the command

find_pair 100mM_hjh.pdb bpfile.dat

and then use that corresponding bpfile.dat.
I found the following thread useful
http://forum.x3dna.org/md-simulations/issues-with-x3dna_ensemble/
Thanks again,
-Clark

[xiangjun]

Hi Clark,

Glad to know that you've solved your problem with x3dna_ensemble. Indeed, one of the intentions of the 3DNA Forum is to create "a pleasant virtual community for all of us to learn from and contribute to."

Best regards,

Xiang-Jun