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Questions and answers => General discussions (Q&As) => Topic started by: slaw on September 06, 2011, 05:44:28 pm

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Title: 3DNA Cannot find help3dna.dat
Post by: slaw on September 06, 2011, 05:44:28 pm

Hi,

I downloaded 3DNA v2.0 and have installed it on a Linux machine.  However, upon executing find_pair I get the error:

open_file </home/seanlaw/X3DNA/config/help3dna.dat> failed: No such file or directory


Of course, find_pair is installed in:

/home/seanlaw/Programs/X3DNA/bin

I'm not sure why find_pair is trying to look in that particular directory and what I can/need to do to have find_pair look in

/home/seanlaw/Programs/X3DNA/config

instead...

Any help or suggestions would be greatly appreciated.  Thanks

Sean

P.S.  I tried searching for help3dna.dat but found nothing.

Title: Re: 3DNA Cannot find help3dna.dat
Post by: xiangjun on September 06, 2011, 09:58:47 pm

Hi Sean,

It is likely that you've not properly set up 3DNA v2.0. Did you run [red:1nrkjhgd]x3dna_setup[/red:1nrkjhgd] as documented in the 2008 3DNA Nature Protocols paper?

More specifically, what's the output from running the following:

Code: [Select]

echo $X3DNABy default, if the [mono:1nrkjhgd]X3DNA[/mono:1nrkjhgd] environment variable is not set, the program will use [mono:1nrkjhgd]$HOME/X3DNA[/mono:1nrkjhgd]. That explains the error message:
[pre:1nrkjhgd]open_file </home/seanlaw/X3DNA/config/help3dna.dat> failed: No such file or directory[/pre:1nrkjhgd]
HTH,

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