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Messages - shahabshariati

Pages: [1]
1
MD simulations / Re: Ruby scripts / where is output file?
« on: April 07, 2011, 09:00:58 am »
Dear temizna

thanks for your reply

I tried by : ruby x3dna_md.rb -b bpfile.dat -e sample_md.pdb -o my.out

but problem was not solved.

I did installation again:

I put x3dna_md_v0.3.tar.gz in /root/parameter directory.

tar -xvzf x3dna_md_v0.3.tar.gz

cd x3dna_md_v0.3

when type ./x3dna_md.rb,

X3DNA environment variable not set.

I used: X3DNA=/root/parameter/x3dna_md_v0.3/X3DNA; export X3DNA

then I typed  ruby x3dna_md.rb -b bpfile.dat -e sample_md0.pdb -o my.out

unfortunately problem was not solved and again, the value of parameter relating to every base pair is the same during trajectory.

please guide me to solve my problem.

best regards.

2
MD simulations / Re: Ruby scripts / where is output file?
« on: April 05, 2011, 05:15:27 am »
Dear xiangjun

I installed x3dna_md_v0.3 again.

after installation, in x3dna_md_v0.3 directory, as you know there are input files (bpfile.dat and sample_md0.pdb) and output file x3dna_md.out.


I used same input files (bpfile.dat and sample_md0.pdb) as follows:


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


unfortunately in my output file (my.out) the value of parameter relating to every base pair is the same during trajectory.

I attached both of x3dna_md.out and my.out files.

what is reason of this problem?

3
MD simulations / Re: Ruby scripts / where is output file?
« on: March 16, 2011, 04:24:40 am »
Dear xiangjun

very thanks for your attention

I installed x3dna_md_v0.3.tar.gz again and then I ran the sample dataset distributed with the Ruby scripts as follows:

 tar -xvzf x3dna_md_v0.3.tar.gz

 cd x3dna_md_v0.3

export X3DNA=/root/ruby_x3dna/X3DNA

 ./x3dna_md.rb -b bpfile.dat -e sample_md0.pdb

output file (x3dna_md.out ) was created but there is a problem.

I attached my output file named my.out.

in my.out file the value of parameter relating to every base pair is the same during trajectory

x3dna_md.out :

<phase1>      # with 12 data columns
0   127.6   105.2   139.4   155.4   136.8   93.2   17.4   137.5   163.8   141.1   152.7   126.5
1   132.1   85.2   141.0   156.7   98.9   124.3   115.7   124.7   115.8   81.8   126.8   86.6
2   158.2   105.0   135.7   154.0   112.6   140.1   95.6   126.1   115.0   125.2   125.0   110.1
3   121.8   127.3   122.8   105.0   115.6   112.6   106.4   150.4   121.6   122.3   104.0   143.9
4   120.1   152.3   154.9   148.1   135.1   107.0   93.1   86.2   121.3   149.9   164.3   118.3
5   144.3   121.9   160.5   101.7   104.4   114.5   117.3   128.8   98.1   116.1   162.2   148.1
6   162.1   146.9   109.9   106.4   124.1   161.0   102.3   118.7   176.6   130.8   171.1   102.7
7   141.4   180.6   120.8   6.0   149.3   130.6   122.7   117.7   66.4   155.4   84.4   162.3
8   168.8   176.5   109.0   142.3   187.4   74.1   121.6   106.6   140.8   117.6   21.5   172.5
9   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
10   128.7   162.7   144.6   95.4   102.0   114.5   134.4   127.7   129.2   107.0   127.8   94.4
11   138.4   143.1   81.5   139.5   109.0   128.9   99.1   83.6   355.0   165.9   109.0   120.0
12   107.0   141.5   145.2   90.3   70.0   135.2   161.8   122.9   99.5   136.1   109.8   109.8
13   137.9   120.4   99.4   130.6   121.2   119.0   80.5   124.6   138.5   95.2   69.3   159.1
14   138.0   113.5   116.2   131.7   100.6   56.8   356.3   152.2   137.4   147.8   50.8   163.1
15   135.1   136.4   109.1   127.4   96.4   147.5   111.6   78.8   122.5   133.8   131.5   126.2
16   155.3   105.7   126.9   120.1   165.8   91.1   138.0   147.2   113.5   130.8   123.9   147.8
17   120.1   170.0   46.7   108.2   129.6   68.5   140.5   153.1   133.2   134.7   98.1   158.7
18   135.7   155.0   181.0   111.7   123.8   106.2   187.6   144.1   110.2   113.1   115.9   186.8
19   98.6   136.2   168.8   131.1   149.3   15.1   147.0   152.9   163.0   95.1   138.6   134.9
20   139.6   150.0   144.0   118.9   127.5   116.5   113.0   107.6   55.1   127.8   110.7   181.6
</phase1>

my.out:

<phase1>      # with 12 data columns
0   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
1   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
2   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
3   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
4   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
5   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
6   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
7   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
8   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
9   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
10   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
11   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
12   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
13   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
14   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
15   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
16   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
17   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
18   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
19   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
20   134.6   133.8   128.8   106.4   91.2   104.7   100.0   98.4   114.6   14.5   358.6   170.8
</phase1>

is my manner wrong?

please guide me about that

best regrads

4
MD simulations / Re: Ruby scripts / where is output file?
« on: March 08, 2011, 07:43:42 am »
excuse me I forgot to attach dna.pdb file. I did to this post.

5
MD simulations / Re: Ruby scripts / where is output file?
« on: March 08, 2011, 07:41:30 am »
Dear xiangjun

very thanks for your reply.

excuse me for delay in my feedback.
I downloaded and reinstalled the revised script v0.2.

When I run the sample dataset distributed with the Ruby scripts (./x3dna_md.rb -b bpfile.dat -e sample_md0.pdb),
it does work and x3dna_md.out was created.

after that I used Ruby scripts for my MD trajectory.

I attached pdb file (dna.pdb). It contains 10 models.

my bpfile.dat is as follows:

dna.pdb
dna.out
    2         # duplex
   13         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   28  0 #    1 | A:...1_:[DC5]C-----G[DG3]:..26_:A  0.20  0.00  0.05  9.04 -1.30
    2   27  0 #    2 | A:...2_:[.DA]A-----T[.DT]:..25_:A  0.09  0.05  1.13  9.08 -1.30
    3   26  0 #    3 | A:...3_:[.DC]C-----G[.DG]:..24_:A  0.20  0.00  0.06  9.04 -1.30
    4   25  0 #    4 | A:...4_:[.DT]T-----A[.DA]:..23_:A  0.09  0.06  1.13  9.08 -1.30
    5   24  0 #    5 | A:...5_:[.DA]A-----T[.DT]:..22_:A  0.09  0.05  1.13  9.08 -1.30
    6   23  0 #    6 | A:...6_:[.DA]A-----T[.DT]:..21_:A  0.09  0.05  1.14  9.08 -1.30
    7   22  0 #    7 | A:...7_:[.DT]T-----A[.DA]:..20_:A  0.09  0.05  1.12  9.08 -1.30
   10   21  0 #    8 | A:...8_:[.DT]T-----A[.DA]:..19_:A  0.09  0.06  1.14  9.08 -1.30
   11   20  0 #    9 | A:...9_:[.DG]G-----C[.DC]:..18_:A  0.20  0.00  0.08  9.04 -1.30
   12   19  0 #   10 | A:..10_:[.DA]A-----T[.DT]:..17_:A  0.09  0.06  1.14  9.08 -1.30
   13   18  0 #   11 | A:..11_:[.DA]A-----T[.DT]:..16_:A  0.09  0.05  1.13  9.08 -1.30
   14   17  0 #   12 | A:..12_:[.DG]G-----C[.DC]:..15_:A  0.20  0.00  0.07  9.04 -1.30
   15   16  0 #   13 | A:..13_:[DG3]G-----C[DC5]:..14_:A  0.20  0.00  0.07  9.04 -1.30
##### Base-pair criteria used:   4.00 15.00  2.50 65.00  4.50  7.50
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (13): 1 - 13  ***broken O3' to P[i+1] linkage***


I used following command:

./x3dna_md.rb -b bpfile.dat -e dna.pdb

after that I have:

Process model #15 / 10
./x3dna_md.rb:96:in `parse_base_pair_parameters': undefined method `[]' for nil:NilClass (NoMethodError)
        from ./x3dna_md.rb:96:in `collect'
        from ./x3dna_md.rb:96:in `parse_base_pair_parameters'
        from ./x3dna_md.rb:468:in `each_with_index'
        from ./x3dna_md.rb:95:in `each'
        from ./x3dna_md.rb:95:in `each_with_index'
        from ./x3dna_md.rb:95:in `parse_base_pair_parameters'
        from ./x3dna_md.rb:203:in `parse_3dna_output'
        from ./x3dna_md.rb:200:in `open'
        from ./x3dna_md.rb:200:in `parse_3dna_output'
        from ./x3dna_md.rb:281:in `process_ensemble_models'
        from ./x3dna_md.rb:272:in `each'
        from ./x3dna_md.rb:272:in `process_ensemble_models'
        from ./x3dna_md.rb:79:in `main'
        from ./x3dna_md.rb:497

no output file was ctreated.

how to fix it? please guide me about that.

best regards.

6
MD simulations / Re: Ruby scripts / where is output file?
« on: February 12, 2011, 03:16:24 am »
Dear xiangjun

excuse me.

when I use ./x3dna_md.rb -b bpfile.dat -e sample_md0.pdb  for sample dataset, I encountered

./x3dna_md.rb:94:in `each': no block given (LocalJumpError)

how to fix it?

7
MD simulations / Re: Ruby scripts / where is output file?
« on: February 12, 2011, 02:46:19 am »
Dear xiangjun

thanks for your attention.

I downloaded x3dna_md_v0.1.tar.gz.

ruby -v ===> ruby 1.8.5 (2006-08-25) [x86_64-linux]

my OS is : x86_64 x86_64 x86_64 GNU/Linux Red Hat Enterprise Linux Server release 5 (Tikanga)

if I run the sample dataset distributed with the Ruby scripts (./x3dna_md.rb -b bpfile.dat -e sample_md0.pdb),

yes, it does work and didn't give any error:


[root@localhost x3dna_md_v0.1]# ./x3dna_md.rb -b bpfile.dat -e sample_md0.pdb
        sample_md0.pdb: with model numbers <= 0
Process model #0 / 21
./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

8
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

9
MD simulations / Re: the sign of minor or major groove width
« on: February 10, 2011, 01:47:28 am »
Dear xiangjun

thanks for your reply.

I want to know there is this possible that groove widths be negative. My mean is in experiment and not in the output from 3DNA or curve.

best regards.

10
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

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Funded by X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids (R24GM153869)

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University