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Messages - oskolkov

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1
General discussions (Q&As) / Re: Building chromosome with fiber
« on: February 18, 2013, 10:29:58 am »
Hi Xiang-Jun,

thank you for your reply, I have 4 Gb RAM and I tried to build human 21 chromosome which contains around 48 000 000 bps. I monitored my memory usage and did not notice that fiber used a lot of memory. Do you think I should try to build it on a computer with more memory?

Cheers!
Nikolay.

2
General discussions (Q&As) / Building chromosome with fiber
« on: February 18, 2013, 06:27:50 am »
Dear all,

I would like to ask if anyone tried to build a structure of whole chromosome with fiber? I tried and got a message "allocation failure 1 in cmatrix()", so I suspect that the sequence was too long. Can anyone recommend me how to build a chromosome with fiber or with any other program? Thank you!

Cheers!
Nikolay.

3
MD simulations / Re: How to properly use x3dna_ensemble?
« on: April 17, 2012, 12:05:27 pm »
Hi Xiang-Jun,

thank you very much for this update! I have tested it, it worked perfectly. Such an enormous relief! Thank you!

Best wishes,
Nikolay.

4
MD simulations / Re: How to properly use x3dna_ensemble?
« on: April 06, 2012, 04:00:14 am »
Thank you very much Xiang-Jun! That would be really helpful. Looking forward to the updated version.

5
MD simulations / Re: How to properly use x3dna_ensemble?
« on: April 05, 2012, 10:09:23 am »
Hi Xiang-Jun,

finally, I figured out that the main parameter I am intereested in doing my DNA simulation is the bending persistence length, which is related to the DNA bending angle theta as <theta^2>=2L/L_p, where L is the contour length of the DNA segment. Thus, I have to calculate theta^2 averaged over all my MD trajectories.

Here come my question. Doing "analyze" of a single snapshot, I get an output file where (at the end) there is an information about helical axis vectors

Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
         for each dinucleotide step

BUT, when I do "x3dna_ensamble analyze" for multiple snapshots, I do not see helical axis vectors in the output file. Is that true, am I doing everything correctly? Is "x3dna_ensamble analyze" still not able to provide the helical axis vectors information despite "analyze" can do it? Looking forward to your reply.

Cheers!
Nikolay.
 

6
MD simulations / Re: How to properly use x3dna_ensemble?
« on: March 28, 2012, 06:31:29 am »
Hi Xiang-Jun,

thank you for the link, I will try to fix the problem with Cygwin. The version of Ruby I am using is

ruby 1.8.7 (2012-02-08 patchlevel 358) [i386-cygwin]

Nikolay

7
MD simulations / Re: How to properly use x3dna_ensemble?
« on: March 27, 2012, 12:29:23 pm »
Dear Xiang-Jun,

I reinstalled X3DNA and this time it worked out. I got the following

$  x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble_example3.out
Process PDB file pdbdir/model_1.pdb     1 / 20
      5 [main] ruby 5276 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_10.pdb    2 / 20
Process PDB file pdbdir/model_11.pdb    3 / 20
      5 [main] ruby 4496 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_12.pdb    4 / 20
Process PDB file pdbdir/model_13.pdb    5 / 20
      5 [main] ruby 2316 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      5 [main] ruby 5512 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_14.pdb    6 / 20
      7 [main] ruby 6132 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_15.pdb    7 / 20
      7 [main] ruby 6120 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_16.pdb    8 / 20
Process PDB file pdbdir/model_17.pdb    9 / 20
      5 [main] ruby 4668 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_18.pdb    10 / 20
      5 [main] ruby 4428 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_19.pdb    11 / 20
Process PDB file pdbdir/model_2.pdb     12 / 20
Process PDB file pdbdir/model_20.pdb    13 / 20
Process PDB file pdbdir/model_3.pdb     14 / 20
Process PDB file pdbdir/model_4.pdb     15 / 20
Process PDB file pdbdir/model_5.pdb     16 / 20
Process PDB file pdbdir/model_6.pdb     17 / 20
      5 [main] ruby 4240 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      5 [main] ruby 4976 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      5 [main] ruby 5384 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
    235 [main] ruby 4256 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      6 [main] ruby 4876 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      5 [main] ruby 4128 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      7 [main] ruby 5096 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      7 [main] ruby 2872 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
      5 [main] ruby 2896 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_7.pdb     18 / 20
      5 [main] ruby 2392 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_8.pdb     19 / 20
      6 [main] ruby 6040 child_info_fork::abort: address space needed by 'etc.so' (0x370000) is already occupied
Process PDB file pdbdir/model_9.pdb     20 / 20



Then I typed
$ x3dna_ensemble extract -a , -f ensemble_example3.out

and got several .out files with base-pair step parameters.

8
MD simulations / Re: How to properly use x3dna_ensemble?
« on: March 27, 2012, 11:43:54 am »
Yes, I am currently using Cygwin version

9
MD simulations / Re: How to properly use x3dna_ensemble?
« on: March 27, 2012, 10:53:16 am »
Hi Xiang-Jun,

thank you for correcting me. Let me decribe step-by-step the commands I am using now

1)cd $X3DNA/examples/ensemble/md/

2) find_pair sample_md0.pdb bpfile.dat

which gives me bpfile the template base pair input file bpfile.dat. My bpfile.dat looks slightly different from the bpfile.dat provided in the examples/ensemble/md. My bpfile.dat has 13 base-pairs, not 12 as in examples/ensemble/md.

3) x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble.out
Process PDB file pdbdir/model_1.pdb     1 / 20
      5 [main] ruby 5696 child_info_fork::abort: address space needed by 'etc.so' (0x250000) is already occupied
      7 [main] ruby 5740 child_info_fork::abort: address space needed by 'etc.so' (0x250000) is already occupied
      7 [main] ruby 3340 child_info_fork::abort: address space needed by 'etc.so' (0x250000) is already occupied
Error in running command: 'C:\Packages\X3DNA/bin/find_pair -s temp_model.pdb nts_list.txt 2> msgfile'
Rerun the command w/o redirection for details

Very strange, now it gives me an error when I apply x3dna_ensemble analyze. It worked perfectly first time.

Regards,
Nikolay.

3)

10
MD simulations / Re: How to properly use x3dna_ensemble?
« on: March 27, 2012, 09:46:47 am »
Hi Xiang-Jun,

everything seems to work perfectly. I used Gromacs' function trjconv to divide the xtc trjectory into separate snapshots, put them to a subdirectory, generated bpfile.dat using find_pair function of 3DNA and the initial pdb-conformation of my DNA segment, and applied x3dna_ensemble analyze script. The output file bp_step.par contains all the local inter- (twist, roll, tilt etc) and intra-base pair step parameters (shear, stretch etc.). As far as I understand, this is the result of averaging with respect to all snapshots, i.e. time averaged, please correct me if I am wrong.

Cheers!
Nikolay.

11
MD simulations / Re: How to properly use x3dna_ensemble?
« on: March 26, 2012, 06:09:33 am »
Dear Xiang-Jun,

thank you very much for your reply! Yes, you are right, I checked and found out that Gromacs can actually devide an xtc-trajectory file into separate pdb files in MODEL/ENDML format. So in fact I can apply "analyze" command to each pdb file/trajectory and find mechanical properties (local ones) of genome segment at each moment of time. In order to get tilt, twist, roll etc. for the whole period of simulation (whole xtc trajectory), I have to read and average the output information from a number of out-files, since as far as I understand X3DNA can provide mechanical information only for one pdb-file but not for a group of pdb-files which form a trjectory, do I understand it correctly? Curves+ can do it for the whole trajectory, but is much more tricky to use compared to X3DNA :)

Regards,
Nikolay.

12
MD simulations / How to properly use x3dna_ensemble?
« on: March 22, 2012, 04:59:46 am »
Dear Xiang-Jun and 3DNA users,

I am doing MD simulations of DNA segment using GROMACS 4.0.5 which produces trajectories as xtc and trr files, please find enclosed the initial structure pdb file, I did not manage to attach xtc trajectory (21 Mb) due to size restrictions. I want to analyze the trajectories in order to obtain twist, roll, tilt etc profiles. I found out that x3dna_ensemble script included into x3dna_2.1beta version can provide this information. Unfortunately, I have difficulty running this script and would like to ask you what exactly I should type in my bash in order to analyze my xtc/trr trajectories? For example, I tried

$  x3dna_ensemble convert trajectory.xtc
{:help=>false, :package=>"amber"}

or

$  x3dna_ensemble convert trajectory.xtc -p gromacs
{:help=>false, :package_given=>true, :package=>"gromacs"}

in order to convert MD trajectories to MODEL/ENDMDL format, which can be later analyzed by "x3dna_ensemble analyze", but without success. Do I need to somehow split my xtc/trr trajectory into separate pdb files and apply analyze afterwards? I am completely lost, please help me. Could you please write exact commands I should type in my bash? Thank you.

With best regards,
Nikolay.

**********************************************************************
Dr. Nikolay Oskolkov
Department of Clinical Sciences, Diabetes and Endocrinology,
CRC, Entr 72, building 91, level 12, University Hospital Malmo
SE-205 02 Malmo, Sweden

Email: Nikolay.Oskolkov@med.lu.se
Tel.:  +46 761463349

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.