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1
MD simulations / Re: local helical axis vector for strongly bent DNA
« Last post by xiangjun on June 21, 2017, 09:50:24 pm »
Check the source code to get to the bottom of the technical details.

For the analysis of NMR ensembles or MD trajectories, however, manually editing 'find_pair'-generated base-pair file may be the preferred way to go, as documented for the 'x3dna_ensemble' script distributed with 3DNA.

Xiang-Jun
2
MD simulations / Re: local helical axis vector for strongly bent DNA
« Last post by adihau on June 21, 2017, 08:28:25 pm »
Thank you very much, I was searching for something like this.

I have one more question.
Is there any possibility to find out, which of those criteria was the one, which caused, that the bases were not matched as pair? And can I find out what values those geometric quantities have?
Because then it would be easier to adjust the criteria in a way that all base-pairs are treated as such.

Thank you,
Adina
3
MD simulations / Re: local helical axis vector for strongly bent DNA
« Last post by xiangjun on June 21, 2017, 03:50:03 pm »
Hi Adina,

Thanks for your follow-up. Your cases occur frequently, especially in the field of MD simulations. Please have a look of the FAQ entry "How to fix missing (superfluous) base pairs identified by find_pair?".

Using your F30 as an example, the two terminal "base pairs" are too far off normal, as can be seen clearly from the attached image. Similar story happens for F29. For such cases, the 3DNA find_pair program won't detect these "presumed" base pairs. This is not a bug, but a feature by design. Users should pay close attention to these missing pairs.

You can force 3DNA to take them as pairs by manually editing the output from "find_pair" before feeding it into "analyze". The find_pair/analyze two-step procedure has been implemented in 3DNA specifically to allow for such flexibility.

HTH,

Xiang-Jun
4
MD simulations / Re: local helical axis vector for strongly bent DNA
« Last post by adihau on June 21, 2017, 01:11:49 pm »
Hi Xiang-Jun,

thanks a lot for your fast reply! And sorry for not attaching the files.
I used the following command 
Code: [Select]
find_pair F29.pdb stdout | analyzeThe results, I get with that are F29-analyze.out and F30-analyze.out

The command you suggested, helps in the case of F29, where the '----' lines are calculated now (F29-analyze-c.out), but there is no change for F30.

The problem is, that this DNA has 10 base-pairs, but in F29-analyze.out it says, there are 9 base-pairs (And in F30-analyze.out it says there are 8 base-pairs). Why does X3DNA not recognize one (two) of the base-pairs?

Thanks for your help,
Adina
5
MD simulations / Re: local helical axis vector for strongly bent DNA
« Last post by xiangjun on June 20, 2017, 07:54:59 pm »
Hi Adina,

Thanks for posting on the 3DNA Forum. Without seeing a concrete example, I can only guess based on experience. Let the structure (a single frame) be named sample.pdb, try the following to see if you can get what you want:

Code: [Select]
find_pair sample.pdb | analyze -c
Note the -c option which treats the detect double helix as a continous unit.

HTH,

Xiang-Jun
6
MD simulations / local helical axis vector for strongly bent DNA
« Last post by adihau on June 20, 2017, 06:49:53 pm »
Hello everyone,

I was analyzing a molecular dynamics simulation (http://www.amber.utah.edu/FF-DNA-bsc1-OL15/3GGI/opc/bsc0/ ) with do_x3dna and noticed, that in the HelAxis_g.dat file for most of the frames one line of data is missing. (sometimes even two lines are missing or replaced by '----'). The DNA contains 10 base-pairs, so there should be 9 helical axis vectors, since they are calculated as base-step parameters.

When I run single frames of the simulation with X3DNA, and look at the local helical axis vector there, I find four different cases.
1. "number of base-pairs: 10" ;  all helical axis vectors are calculated.
2. "number of base-pairs: 9"  ; the helical axis vector for one base-pair step is missing.
3. "number of base-pairs: 8"  ; the helical axis vectors for two base-pair steps are missing.
4. "This structure has broken O3'(i) to P(i+1) linkages"  and   "number of base-pairs: 9"  ; 
     the helical axis vector of one base-pair step is missing and in another line the data is replaced by '----'.

My explanation for this is, that if the program detects a broken base-pair, it refuses to calculate any vectors and prints '----' instead. Also it seems, that if the DNA is deformed or broken too much, then the program doesn't recognize this as a base-pair anymore and thinks the DNA is shorter than it actually is.

My question is now: Is there any way to force the program to still calculate a helical axis vector, even if the DNA is strongly bent and/ or broken?
And if yes, does maybe someone know, how to implement this into the do_x3dna program?

Thank you very much for your help,
Adina
7
The error message shows some variables (e.g., LIBFFTW etc) are not set. Presumably you need to install additional libraries, which are nevertheless not required by 3DNA per se. You may need to contact the author(s) of do_x3dna for further details.

Xiang-Jun
8
MD simulations / problem regarding installation of do_X3DNA
« Last post by sacky0003 on June 17, 2017, 02:50:12 am »
Dear users,

I have installed cmake-3.9, fftw-3.3.6,x3dna-v2.3.
But when I am trying to install do_X3DNA it shows error.
I have followed this steps:
1.tar xfz do_x3dna-master.tar.gz     .... works fine
2. cd do_x3dna                                  .....works fine
3.mkdir build                                         .......works fine
4.cd build                                              .......works fine
5.cmake ..  -DGMX_PATH=/opt/gromacs -DCMAKE_INSTALL_PREFIX=/opt/do_x3dna  .... errors occurred

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
LIBFFTW
    linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src
LIBGMX
    linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src
LIBGMXANA
    linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src
LIBMD
    linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src

-- Configuring incomplete, errors occurred!
See also "/home/saikat/gromacs/do_x3dna-master/build/CMakeFiles/CMakeOutput.log".


what should i do ?? help me out

Thanks and regards

Saikat
9
MD simulations / Re: Analysis of Amber .mdcrd File
« Last post by xiangjun on June 15, 2017, 12:07:32 pm »
3DNA starts from the standard MODEL/ENDMDL ensemble PDB format, as for NMR structures. It does not work directly from an AMBER trajectory file, or other specialized MD formats. However, it should be feasible to convert MD-specific formats to the standard PDB ensemble format. For torsional anlge calculations, you may want to try DSSR (which has the --nmr option).

Alternatively, you may try do_x3dna, or Curves+.

Xiang-Jun
10
MD simulations / Re: Analysis of Amber .mdcrd File
« Last post by sacky0003 on June 15, 2017, 11:47:47 am »
Dear sir,

I am using AMBER package. I want to know is it possible to calculate Torsional angle wheel for average angles of segment of a bound and an unbound DNA from AMBER trajectory file (.mdcrd) ??

Thanks and regards.

saikat
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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.