Issues related to 3DNA and the MD Ruby scripts set up

[HenryFisher]

Hi Xiang-Jun

I have been using x3dna recently and trying to get used to working in MinGW.  I have had some success and managed to produce a DNA molecule in a .pdb file.  However I am interested in building ssRNA molecules preferably with a theoretical secondary structure for use in AMBER MD.  I registered a couple of days ago and you recommended I use the ruby scripts for MD.  I have downloaded these scripts and extracted them to my X3DNA folder.  The first problem I encountered was when trying to run the x3dna_md.rb file with the recommended first command

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x3dna_md.rb -b bpfile.dat -e sample_md0.pdb This returned the error

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/usr/bin/env: ruby: No such file or directory  I think I fixed this by installing ruby, at least I don't get that error any more.  Now when I try to execute the command above I get

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X3DNA environmental variable not set I don't know what this means but I tried to resetting the path for X3DNA

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export X3DNA=/usr/local/X3DNA/
export PATH=$PATH:$X3DNA/bin But this didn't work.  Any help would be greatly appreciated, I hope there's enough information here, if not please let me know.  This is my first time using a Linux based command programme so I'm sorry if I've done something really stupid.

Thanks
Henry Fisher

[HenryFisher]

Since writing the above post I have followed some instructions from another post:

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export X3DNA=/usr/home/bshcf/X3DNA
export PATH=$PATH:$X3DNA/bin
chmod a+rx /usr/home/bshcf/X3DNA/bin/*
find_pair find_pair displayed the help file as expected however when using:

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x3dna_md.rb -b bpfile.dat -e sample_md0.pdb I now get another error

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3DNA settings error: can't execute C:/MinGW/msys/1.0/home/bshcf/X3DNA/bin/analyze

[xiangjun]

Hi Henry,

Thanks for using 3DNA. I fully understand how frustrated it could be to get a new software system up and running, and you are welcome to ask any 3DNA-related questions in the forum.

The Ruby scripts may be useful if you are using AMBER for MD simulations. For building general sequence single strand RNA structures, the recent post "building a ssDNA" may help. Run also "fiber -m" to see all available fiber RNA models.

Regarding the specific problem you have with running the Ruby script '[mono:1bnxcgla][red:1bnxcgla]x3dna_md.rb[/red:1bnxcgla][/mono:1bnxcgla]':
[pre:1bnxcgla]3DNA settings error: can't execute C:/MinGW/msys/1.0/home/bshcf/X3DNA/bin/analyze[/pre:1bnxcgla]
It is likely due to line #425:
[pre:1bnxcgla]fatal("3DNA setting error: can't execute #{x}") unless File.executable?("#{x}")[/pre:1bnxcgla]
change it to (i.e., by adding [mono:1bnxcgla][red:1bnxcgla].exe[/red:1bnxcgla][/mono:1bnxcgla] at the end since you are using MinGW)
[pre:1bnxcgla]fatal("3DNA setting error: can't execute #{x}") unless File.executable?("#{x}[red:1bnxcgla].exe[/red:1bnxcgla]")[/pre:1bnxcgla]
Have a try, and report back how it goes.

Generally speaking, the best way to get started with 3DNA is by reading the 2008 3DNA Nature Protocols paper, and working out the recipes.

HTH,

Xiang-Jun
[hr:1bnxcgla][/hr:1bnxcgla]
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