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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
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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 (http://forum.x3dna.org/general-discussions/x3dna_ensemble-is-not-working-for-hairpin-loop-structures/msg2051/#msg2051)"
Xiang-Jun
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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
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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
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University