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Questions and answers > MD simulations
H-bonding information in MD analysis output
Andre:
Hi All,
I have used the x3dna_md.rb script and it has worked perfectly. However, is there a H-bond parameter that it will analyse? I cannot see any H-bond information in the x3dna_md.out file.
Kind regards,
Andre
xiangjun:
Hi Andre,
First, thanks for posting your question in the forum! The more user feedback, the merrier.
Second, you may notice that I have split your post from the thread "Ruby scripts for the analysis of MD simulation trajectories" which is too long (18 posts now), and spans two pages. I have added a new subject line "Re: H-bonding information in MD analysis output" for the new thread.
Third, and more relevant to your question, are you referring to adding a new section for the H-bonding information? An example would be:
<hbond>
1 C-----G [2] O2 - N1 2.99 N4 - O6 2.98
2 C-----G [3] O2 - N2 2.74 N3 - N1 2.84 N4 - O6 3.17
3 T-----A [2] N3 - N1 3.09 O4 - N6 2.86
4 A-----T [2] N1 - N3 2.78 N6 - O4 3.05
5 A-----T [2] N1 - N3 2.81 N6 - O4 2.76
6 T-----A [2] N3 - N1 2.71 O4 - N6 3.06
7 A-----T [2] N1 - N3 3.12 N6 - O4 3.12
8 G-----C [2] N1 - N3 3.00 O6 - N4 2.75
9 A-----T [2] N1 - N3 2.93 N6 - O4 3.12
10 A-----T [2] N1 - N3 2.90 N6 - O4 2.93
11 A-----T [2] N1 - N3 3.01 N6 - O4 3.05
12 T-----A [2] N3 - N1 2.80 O4 - N6 3.12
</hbond>
If that's the case, then it won't be much a problem to parse and add it into the output file. Otherwise, please provide a concrete example to show exactly what you mean.
Please confirm.
Xiang-Jun
Andre:
Dear Xiang-Jun,
Thankyou for the quick reply.
Yes, I would like to have a new section with the H-bonding information in the output file, I am not familiar with ruby, and do not know how to do this using the x3DNA_md.rb script. There are 100 md*.out files to process for a given structure and the script has been very helpful in collecting the DNA parameters.
Kind regards,
Andre
xiangjun:
Hi Andre,
Thanks for your feedback. I will add a section of H-bond parameters (hopefully) by tomorrow, and then release an updated version of the Ruby scripts. So stay tuned, and check back the forum.
Xiang-Jun
Andre:
Dear Xiang-Jun,
Thankyou very much for that. Greatly appreciated.
Kind regards,
Andre
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
