Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Use of Ensemble function  (Read 647 times)

Offline clarkt

  • regular
  • *
  • Posts: 2
    • View Profile
Use of Ensemble function
« on: February 19, 2017, 03:47:21 pm »
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

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1214
    • View Profile
    • 3DNA homepage
Re: Use of Ensemble function
« Reply #1 on: February 19, 2017, 05:49:59 pm »
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
« Last Edit: February 19, 2017, 05:54:58 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline clarkt

  • regular
  • *
  • Posts: 2
    • View Profile
Re: Use of Ensemble function
« Reply #2 on: February 20, 2017, 10:43:54 am »
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

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1214
    • View Profile
    • 3DNA homepage
Re: Use of Ensemble function
« Reply #3 on: February 20, 2017, 12:06:13 pm »
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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.