3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: far217 on December 26, 2006, 05:13:48 pm

Title: can't reproduce example with rebuild
Post by: far217 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.
Title:
Post by: xiangjun 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
Title:
Post by: far217 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.