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Questions and answers => MD simulations => Topic started by: naserian on December 08, 2012, 12:46:36 pm

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Title: Base stacking from x3dna_ensemble
Post by: naserian on December 08, 2012, 12:46:36 pm

Dear Dr. Lu,

I used x3dna_ensemble Ruby script to obtain base stacking information from a PDB MODEL/ENDMDL ensemble (for B-DNA conformation). Although the temp_model.out have information about origin and mean normal vector of each base-pair, but unfortunately the ensemble output does not contain such information. Could you please provide me a solution for this problem?

Many thank,
Ali

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on December 08, 2012, 08:48:13 pm

Hi Ali,

Thanks for using 3DNA and posting your questions on the forum. With feedbacks from users like you, 3DNA can only become more useful to the community.

I think I understand your question: the 3DNA analyze program includes a section as below:

****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
   the coordinate system of the given structure

      bp        Ox        Oy        Oz        Nx        Ny        Nz
    1 C-G      17.13     25.96     25.88     -0.10     -0.44     -0.89
    2 G-C      16.56     24.81     22.95     -0.21     -0.33     -0.92
    3 C-G      16.16     23.97     19.28     -0.18     -0.48     -0.86
...........................................................................

However, the parameters herein are not in x3dna_ensemble output. Am I right?

That section is currently not parsed by the x3dna_ensemble script -- you are the first to make this request. I will consider to add the portion in x3dna_ensemble output in the next release of 3DNA v2.1(beta) in the near future. What format do you prefer?

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: naserian on December 09, 2012, 04:16:08 am

Hi Xiang-Jun,

Thank you very much for your reply. The problem is exactly what you understand. In fact, I want to calculate the number of inter- and intrastrand base stacking for a DNA under stretch. My calculations uses a geometrical criterion that two bases are stacked when the distance between the centers of the rings is <0.45 nm, and the angle between the normals to the bases is <30 degree (based on the information obtained by 3DNA for the origin and mean normal vector of each base-pair). Then, I will plot the variations of number of base stackings as a function DNA length (or simulation time). I hope these explanations are sufficient.

Thanks,
Ali

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on December 09, 2012, 08:48:26 pm

Hi Ali,

Thanks for clarifying your question and providing further details on what you aim to achieve.

Following my previous reply, I've revised the Ruby script associated with x3dna_ensemble to parse the section "Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure". The two newly-added parameters to extract are: bpo_xyz and bpn_vec. Please download 3DNA v2.1(2012dec09) and let me know if that fits the bill.

Since you are interested in base stacking interactions, your may also want to check the section "Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step."

HTH,

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: naserian on December 10, 2012, 04:13:41 am

Hi Xiang-Jun,

Thank you for your update ans suggestion. I encountered a problem with new release of 3DNA at the first step, i.e. when I used “find_pair”. When I tried

>> find_pair actg3_md.pdb bpfile.dat

I got errors such as follows

-----
no matching entry for atom name [] (...) in 'atomlist.dat'
   now it is set as 'XX'
   check and update file $X3DNA/config/atomlist.dat
-----

actg3_md.pdb is a PDB MODEL/ENDMDL ensemble created by AmberTool12 (the PDB file is attached). By the previous release (2012Nov26) there is not any problem!
When I used bpfile.dat (created by the previous release of 3DNA) with “x3dna_ensemble” of the current release to see the changes you added (>> x3dna_ensemble analyze -b bpfile.dat -e actg3_md.pdb -o ensemble.out), I got the following error:

-----
mismatch between base-pair info and model file
-----

Would please help me? The bpfile.dat file is attached too.
Is it not possible that 3DNA analyze directly the output trajectory file of famous MD codes such as Amber?

With best regards,
Ali

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on December 10, 2012, 08:02:48 am

Thanks for letting me know the new issues you experienced -- I will look not them and get back to you shortly.

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on December 10, 2012, 01:17:01 pm

Hi Ali,

Thanks for providing a sample AMBER MD trajectory file (actg3_md.pdb) which allow me to trace where the problem is.

A portion of PDB ATOM record from the file is as below:

Code: [Select]

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM     11  N9  DA5     1       0.781  -4.705  -0.553  0.00  0.00             
ATOM     12  C8  DA5     1      -0.573  -5.051  -0.401  0.00  0.00             
ATOM     13  H8  DA5     1      -0.879  -6.079  -0.526  0.00  0.00             
ATOM     14  N7  DA5     1      -1.349  -3.982  -0.328  0.00  0.00             
ATOM     15  C5  DA5     1      -0.421  -2.977  -0.164  0.00  0.00             
ATOM     16  C6  DA5     1      -0.512  -1.582   0.086  0.00  0.00       
According to the PDB format specification (http://deposit.rcsb.org/adit/docs/pdb_atom_format.html), columns 55 to 60 [Real(6.2)] is for atom occupancy. Normally, it is 1.00 -- check one of PDB entries (e.g., 355d (http://www.rcsb.org/pdb/explore/explore.do?structureId=355d)) for an example. Now, as you can see, AMBER puts 0.00 there. It happens that in the 2012dec09 release of 3DNA, I added checking for atom occupancy (see "What's new? (http://x3dna.org/about/what-is-new)" for details). It is in that release that atoms with zero occupancy are ignored -- so find_pair would judge that your MD trajectories contains no base pairs. That explains your observation:

Quote

By the previous release (2012Nov26) there is not any problem!

You raised an interesting question:

Quote

Is it not possible that 3DNA analyze directly the output trajectory file of famous MD codes such as Amber?

Surely I'll like to make 3DNA directly applicable to the output trajectory file of the famous AMBER package. So I have now made checking for -occupancy optional that can be turned on by user explicitly. Download the updated 3DNA v2.1 2012dec10 release, and it should have solved the problem.

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: naserian on December 11, 2012, 03:49:20 am

Thank you very much for your responses and your good software.

Best wishes,
Ali

Title: Re: Base stacking from x3dna_ensemble
Post by: naserian on December 13, 2012, 10:24:53 am

Hi Xiang-Jun,

My DNA stretching simulations result in conformations in which some interstrand base stackings can be seen (please see attached snapshot). To determine the interstrand base stacking or temporary itrastrand base stacking interaction made in non-canonical conformation of double stranded DNA, I think information about position of center of bases on each strand and their normal vector are needed.  Could you please add such information to the outputs of 3DNA?

Thank you,
Ali

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on December 13, 2012, 11:03:57 am

What do you mean exactly by "position of center of bases"? Geometric center of all base atoms, or just ring atoms? I may consider to add such info that can meet your needs and fit into other parts of 3DNA.

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: naserian on December 13, 2012, 02:09:22 pm

Thank you for your reply. I mean geometric center of ring atoms.

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on December 15, 2012, 12:14:16 pm

The updated 3DNA v2.1 (2012dec15) should do the trick for you. In particular, I added the -ring option to 'analyze' and the corresponding 'x3dna_ensemble analyze' script. By default, the -ring option is not set for back compatibility. So other users won't notice any differences.

For example, in directory $X3DNA/examples/ensemble/md, you can run the following command:

Quote

x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb -r

Note the -r option (short-hand form for -ring).

When you run x3dna_ensemble extract -l, you will find the new parameters are named as below:

Code: [Select]

[ 5] b1c_xyz             [ 6] b1n_vec             [ 7] b2c_xyz             [ 8] b2n_vec
Please verify and report back how it goes.

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: naserian on December 16, 2012, 11:13:36 am

Dear Dr. Lu,

It seems that everything is fine. Thank you very much.

All the best,
Ali

Title: Re: Base stacking from x3dna_ensemble
Post by: dauss75 on April 01, 2013, 11:49:04 am

Dear Xiang-Jun,

Thanks so much for your contribution making the program useful and keeping updated.

I have a follow-up question on this thread.
I wanted to calculate base stacking on a single strand in RNA.  Using the -ring option, I could
extract information of the origin and normal vectors (b1c, b2c, b1n, and b2n)
of each strand following 5' -->3' direction.

After the calculations of distance and angle between bases, I find the distance values make sense, but the angle seems too small.
The equation I use to compute is:
theta  = arccos (dot(n1,n2)) where n1 and n2 are normal vectors from the b1n file

I wonder whether the angle I am getting is in radians?

Regards,

Jung

Title: Re: Base stacking from x3dna_ensemble
Post by: xiangjun on April 01, 2013, 12:06:03 pm

Quote

theta  = arccos (dot(n1,n2)) where n1 and n2 are normal vectors from the b1n file

I wonder whether the angle I am getting is in radians?

You are getting the angle in radians instead of degrees. To verify, let n1 = [1, 0, 0]; n2 = [0, 0, 1], the angle should be 90 degrees.

Xiang-Jun

Title: Re: Base stacking from x3dna_ensemble
Post by: dauss75 on April 01, 2013, 02:24:30 pm

Many thanks.

I should've verified by using the trick you noted here.

Regards,

Jung

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