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Author Topic: Unnatural base pair helical parameters  (Read 252 times)

Offline sarkagaku

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Unnatural base pair helical parameters
« on: September 09, 2020, 05:46:09 pm »
Dear Dr. Xiang,

I did a molecular dynamics simulation for DNA with modified base pairs using gromacs. I wanted to analyze base pair parameters for each base pair.

I tried to use 3DNA also, but it also gave errors.
find_pair -p onesb_frame1.pdb allbp_list

handling file <onesb_frame1.pdb>
Match 'IUG' to 'a' for residue IUG    6  on chain   [#6]
    check it & consider to add line 'IUG     a' to file <baselist.dat>
Match 'JSP' to 'u' for residue JSP   19  on chain   [#19]
    check it & consider to add line 'JSP     u' to file <baselist.dat>
missing ' N1 ' atom : residue name 'JSP', chain  , number [  19 ]
missing ' C5 ' atom : residue name 'JSP', chain  , number [  19 ]
Cannot identify RN9/YN1 in [JSP] -- use atom [ C1 ] instead
missing ' N1 ' atom in base ring atoms
missing ' C5 ' atom in base ring atoms
missing ' N1 ' atom : residue name 'JSP', chain  , number [  19 ]


Do let me know how to calculate base pair parameters including major and minor groove parameters. There was one example in your homepage, but its not working in my case.

Thank you very much
Regards
A Shaikh

Offline xiangjun

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Re: Unnatural base pair helical parameters
« Reply #1 on: September 09, 2020, 08:29:51 pm »
Dear Dr. Shaikh,

Based on the PDB files you attached, the 3DNA find_pair program is working as expected with the -p option.

Quote
Do let me know how to calculate base pair parameters including major and minor groove parameters. There was one example in your homepage, but its not working in my case.

You need to run find_pair without the -p option, and feed the base-pairs list to the analyze program, as shown below:

Code: Bash
  1. find_pair onesb_frame1.pdb pairs_list.txt
  2. analyze pairs_list.txt
  3. # or combined as below:
  4. find_pair onesb_frame1.pdb | analyze

You may want to read the 2008 3DNA Nature Protocols paper, and the 2013 JoVE paper. See also the previous thread "Failed Downloading MD Ruby Scripts of 3DNA". You may want to give DSSR 2.0 a try: see the Overview PDF.

Best regards,

Xiang-Jun

Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline sarkagaku

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Re: Unnatural base pair helical parameters
« Reply #2 on: September 10, 2020, 05:23:05 am »
Dear Dr. Xiang-Jun
Thank you for reply.
Can we apply this method to gromacs trajectory or amber trajectory. Or can we use multiple pdb frames to calculate helical parameters.
Thanks for DSSR, I have installed the program, going through the manual.

Thanks
Regards
Shaikh

Offline xiangjun

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Re: Unnatural base pair helical parameters
« Reply #3 on: September 10, 2020, 08:18:18 am »
Hi Shaikh,

Quote
Can we apply this method to gromacs trajectory or amber trajectory. Or can we use multiple pdb frames to calculate helical parameters.

Follow my previous response, you should be able to find the answers to these questions. For your own understanding and the benefit of other viewers, please post back what you find.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline sarkagaku

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Re: Unnatural base pair helical parameters
« Reply #4 on: September 10, 2020, 11:57:23 am »
Hi

I used x3dna-dssr to get json file using following command. Pdb conatins 100 frames.

x3dna-dssr -i=bdna1-100.pdb -o=bdna.json --more --nmr --json

Once I got json file, I tried to use Markus's R script to extract the data. I installed dplyr and tidyjson library required for the script.
http://forum.x3dna.org/rna-structures/dssr-analyzing-nmr-structures-overwritten-output-files/

However, I am not getting any output.
R -s -f dssr_json_example-v3.R

Following is the output
Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Attaching package: ‘tidyjson’

The following object is masked from ‘package:stats’:

    filter

Warning message:
In gather_array(.) :
  array.index column name already exists, changing to array.index.2
# A tbl_json: 0 x 17 tibble with a "JSON" attribute
# … with 17 variables: ..JSON <chr>, document.id <int>, array.index <int>,
#   array.index.2 <int>, chain <chr>, id <chr>, resi <chr>, resn <chr>,
#   alpha <dbl>, beta <dbl>, gamma <dbl>, delta <dbl>, epsilon <dbl>,
#   zeta <dbl>, chi <dbl>, baseSugar_conf <chr>, sugar_class <chr>

I don't know what is wrong. I am new to R language.
Any suggestion from your side.
Thank you
A Shaikh

Offline sarkagaku

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Re: Unnatural base pair helical parameters
« Reply #5 on: October 03, 2020, 07:50:35 am »
Hi

Finally succeed in calculating helical base parameters for unnatural base pairs.
I used following procedure
1) converted gromacs trajectory to amber trajectory format using Amber CPPTRAJ
2)  Used modified cpptraj for unnatural base pairs
https://github.com/Amber-MD/cpptraj/pull/806

Thanks
Regards
Shaikh

 

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.