Messages

1

MD simulations / Re: Ruby scripts for the analysis of MD simulation trajector

« on: October 11, 2013, 02:20:04 pm »

ok,

so, the thing is that... is just that this script is now called x3dna_ensemble.

I had installed the x3dna correctly, just look this lines in my root (terminal)

~/3dna/x3dna-v2.1/bin$ ls
  anyhelix      comb_str   find_platform  o1p_o2p   regular_dna  step_hel              x3dna_setup
  blocview      ex_str     frame_mol      pdb2img   rotate_mol   x3dna_ensemble        x3dna_utils
alc2img   bp_order.dat  fiber      get_part       r3d_atom  stack2img    x3dna_md_v0.7
analyze   cehs          find_pair  mutate_bases   rebuild   std_base     x3dna_md_v0.7.tar.gz

entering into the directory

~/3dna/x3dna-v2.1/bin/x3dna_md_v0.7$ ls
examples  extract_par.rb  README  trollop.rb  x3dna_md.rb

but you tell me that it isn't the correct script and now it has other name

so now I will  check your help and report to the forum

thanks

jorge

2

MD simulations / Re: Ruby scripts for the analysis of MD simulation trajector

« on: October 11, 2013, 06:23:54 am »

hello friends

  I have a problem when I try run the Ruby scripts for the analysis of MD simulation trajectory

 I follow the instructions of README text.

EXAMPLES

        Change to the sub-directory 'examples/' under your installation of the
        scripts (e.g., x3dna_md_v0.6/examples), then:

                x3dna_md.rb -b bpfile.dat -e sample_md0.pdb -o my.out
          or
                ../x3dna_md.rb -b bpfile.dat -e sample_md0.pdb -o my.out
          and
                diff x3dna_md.out my.out

---------------------------------------------------------------------------------------------------------

~/3dna/x3dna-v2.1/bin/x3dna_md_v0.7/examples$ x3dna_md.rb -b bpfile.dat -e sample_md0.pdb -o my.out
x3dna_md.rb: not order found

--------------------------------------------------------------------------------------------------------
but, I don't know exactly what happen ...

also try the follow, and the messege is :

:~/3dna/x3dna-v2.1/bin$ ./x3dna_md.rb
X3DNA environmental variable not set

please, any help will be appreciated

jorge

 

3

General discussions (Q&As) / Re: how to run 3dna scripts

« on: October 07, 2013, 01:46:49 am »

Thanks Xiang-Jun

 I will try to do what you say me  and  come back to write to you , in case that I fail again, and report to forum about situation

Jorge

4

General discussions (Q&As) / how to run 3dna scripts

« on: October 05, 2013, 08:58:51 pm »

Dear Friends;

   Hi my name is Jorge, I am from Chile and I send you this e-mail  because, following your guide (3dna.pdf) step by step, & when I arrive to section "2.3 bin"   I installed once the 3DNA, I try execute anyone script (see PD:) that are into bin folder, but I fail and I do not Know why =( ... to give you an Idea,  in the root I am here :

me@PC: ~/Desk/3dna/v1.5/src/X3DNA/bin$ ls

alc2img           cehs           dcmnfile      fiber              get_part       nmr_ensemble   pdb2img      regular_dna    std_base      analyze       block_atom    comb_str      del_ms             find_pair   manalyze       nmr_strs      r3d_atom     rotate_mol      step_hel       anyhelix          stack2img
blocview          cp_std        ex_str         frame_mol      mstack2img  o1p_o2p           rebuild 

I find the same that you say in the guide

"This directory contains executables of the 3DNA package. Most of which are utility programs with some in short Perl script. Detailed usage of each program is described in Section 3."

section 3 say How to run 3DNA : Running 3DNA is simple ...

 =(  I don't feel good for this, is not  easy to me apparently

so the questions are :

1.- how to run this programs? wich is the formula or protocol?

2.-  I need any enviroment to execute these ?

3.- could you help me perhaps with oriantation about to my dificulties ?

4.- wich is the next step ?  am I doing something bad in the procedure ?


blessings

Jorge