Topics

1

MD simulations / Ruby scripts / where is output file?

« on: February 10, 2011, 09:32:10 am »

Dear all

I want to use Ruby scripts for obtaining helical parameters of dna during md simulation.

at first, I downloaded from http://3dna.rutgers.edu:8080/data/x3dna_md_v0.1.tar.gz.

I installed that in /root/3dna such as after installation, /root/3dna/x3dna_md_v0.1

I obtained bpfile.dat by find_pair :

3dna.pdb
3dna.out
    2         # duplex
   13         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   26  0 #    1 | ...1>-:...1_:[DC5]C-----G[DG3]:..26_:-<...1
    2   25  0 #    2 | ...1>-:...2_:[.DA]A-----T[.DT]:..25_:-<...1
    3   24  0 #    3 | ...1>-:...3_:[.DC]C-----G[.DG]:..24_:-<...1
    4   23  0 #    4 | ...1>-:...4_:[.DT]T-----A[.DA]:..23_:-<...1
    5   22  0 #    5 | ...1>-:...5_:[.DA]A-----T[.DT]:..22_:-<...1
    6   21  0 #    6 | ...1>-:...6_:[.DA]A-----T[.DT]:..21_:-<...1
    7   20  0 #    7 | ...1>-:...7_:[.DT]T-----A[.DA]:..20_:-<...1
    8   19  0 #    8 | ...1>-:...8_:[.DT]T-----A[.DA]:..19_:-<...1
    9   18  0 #    9 | ...1>-:...9_:[.DG]G-----C[.DC]:..18_:-<...1
   10   17  0 #   10 | ...1>-:..10_:[.DA]A-----T[.DT]:..17_:-<...1
   11   16  0 #   11 | ...1>-:..11_:[.DA]A-----T[.DT]:..16_:-<...1
   12   15  0 #   12 | ...1>-:..12_:[.DG]G-----C[.DC]:..15_:-<...1
   13   14  0 #   13 | ...1>-:..13_:[DG3]G-----C[DC5]:..14_:-<...1
##### Base-pair criteria used:   4.00   0.00  15.00   2.50  65.00   4.50   7.50 [ O N]
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (13): 1 - 13

the name of pdb file is 3dna.pdb (containing 41 models)

I put bpfile.dat and 3dna.pdb files in /root/3dna/x3dna_md_v0.1.

I used following command like what is in viewtopic.php?f=11&t=195.

./x3dna_md.rb -b bpfile.dat -e 3dna.pdb -o 3dna.out after that I have:

        3dna.pdb: with model numbers <= 0
Process model #0 / 41
./x3dna_md.rb:94:in `each': no block given (LocalJumpError)
        from ./x3dna_md.rb:94:in `parse_base_pair_parameters'
        from ./x3dna_md.rb:466:in `each_with_index'
        from ./x3dna_md.rb:93:in `each'
        from ./x3dna_md.rb:93:in `each_with_index'
        from ./x3dna_md.rb:93:in `parse_base_pair_parameters'
        from ./x3dna_md.rb:201:in `parse_3dna_output'
        from ./x3dna_md.rb:198:in `open'
        from ./x3dna_md.rb:198:in `parse_3dna_output'
        from ./x3dna_md.rb:279:in `process_ensemble_models'
        from ./x3dna_md.rb:270:in `each'
        from ./x3dna_md.rb:270:in `process_ensemble_models'
        from ./x3dna_md.rb:77:in `main'
        from ./x3dna_md.rb:495

there is no error but I didn't find my output file (3dna.out)

is my manner true?

please guide me about finding of output file.

best regrads

2

MD simulations / the sign of minor or major groove width

« on: February 09, 2011, 07:31:39 am »

Dear all

I did MD simulation of DNA by amber. Then I obtained minor or major groove width by cur+ and canal.

in output relating to minor or major groove width, there are number with negative sign. can width values be negative?
are my output file wrong? if so, how to fix it?

is there problem in cur+ and canal program.

If I obtain above parameters with 3DNA, there isn't same problem. is it true?

please guide me.

best regards