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Author Topic: can't reproduce example with rebuild  (Read 4874 times)

Offline far217

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can't reproduce example with rebuild
« on: December 26, 2006, 05:13:48 pm »
Hello,
I'm trying to rebuild my DNA structure and I can't. I can't even rebuild the structures in the Example/Analyze_rebuild directory.
I tried to follow the example you've got in the FAQs on How do I build a nucleic acid structure with a sugar-phosphate backbone?
I have the following error when I run rebuild -atomic bp_step.par bdl084_3dna.pdb

error:
cannot open input file -atomic

which is the same I've got for my DNA molecule. If I remove the -atomic option I have:

unknown residue ***local

Any thoughts?
Thank you,
fabian.

Offline xiangjun

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« Reply #1 on: December 27, 2006, 10:36:43 pm »
Hi,

This is weird -- it certainly should not happen as far as 3DNA itself is concerned. I suspect that you have another program called "rebuild" in your command line search path, and it is ahead of $3DNA/bin.

To verify, try:
Code: [Select]
which rebuild from your shell prompt. What do you get?

Alternatively, try to run $3DNA/bin/rebuild instead of just "rebuild".

Have a try and please let me know how it goes.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline far217

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« Reply #2 on: December 29, 2006, 03:00:28 pm »
yes Xiang-Jun, I had another rebuild command from another package software before the rebuild from 3dna. Thank you for the help. I didn't realize of that.

fabian.

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.