Messages

1

General discussions (Q&As) / Re: Use of Ensemble function

« 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

2

General discussions (Q&As) / 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