3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Anju Sharma on May 16, 2007, 01:57:52 am

Title: Unable to generate .out file by using analyze command
Post by: Anju Sharma on May 16, 2007, 01:57:52 am: Hello

Please ignore the queries posted by me earlier to this. After reading similar prblms in d forum nd solutions provided to them i am able to convert my .pdb file to .inp file

But again m struck at next step, while trying to analyze my DNA seq using command:
# analyze atc.inp

no main parameter output file is generated (.out). where is the fault please do let me know.

files that are being generated are:
atc.inp bp_order.dat col_helices.scr ref_frames.dat
auxiliary.par bp_step.par hel_regions.pdb stacking.pdb
bestpairs.pdb cf_7methods.par hstacking.pdb
bp_helical.par col_chains.scr poc_haxis.r3d
Title:
Post by: xiangjun on May 16, 2007, 10:34:04 pm: Thanks for using 3DNA! I am glad that you solved your two previous problems by browsing the forum -- that's exactly why the forum was created in the fist place.

While 3DNA is not a point-and-click package, setting it up should be straightforward and requires minimum effort, i.e., by setting the environment variable X3DNA and put $X3DNA/bin into your command line search path. To make life even easier for inexperienced Linux/Unix users, I have created a Perl script (setup_x3dna) to detect the SHELL and set up these two items automatically -- it will be included in the coming new release.

Now come to your question. The main output file name is derived from your PDB file by changing to (or appending) the ".out" extension. It will be in the same directory as your PDB structure file. Have a look at .inp file -- the 2nd line will tell you where the .out resides. Now I notice a bit of inconsistency here -- all other files are written in the current working directory (CWD), but this .out file is not. Maybe it is more logical to put the .out file in the CWD as well. I will make this change into the new release of 3DNA.

HTH,

Xiang-Jun