normal Building CG DNA using martinize-dna.py

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5 years 2 months ago #3608 by doa.hawamdeh
Building CG DNA using martinize-dna.py was created by doa.hawamdeh
Hello,

I'm trying to build the coarse grained DNA using martinize-dna.py. I wrote : python martinize-dna.py -dnatype ds -f 2M8Z.pdb -o cg.top -x cg.pdb
and this resulting in this error: File "martinize-dna.py", line 4787, in <module>
main(options)
File "martinize-dna.py", line 4298, in main
order, merge = check_merge(chains, options, options, options and options)
File "martinize-dna.py", line 2500, in check_merge
merges = [[(i.isdigit() and int(i) or dct+1)-1 for i in j] for j in m_list]
KeyError: 'B'
What does this mean? Please can you help me in solving this problem?

Doa'

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5 years 2 months ago - 5 years 2 months ago #3609 by jaakko
Replied by jaakko on topic Building CG DNA using martinize-dna.py
Hi Doa,

I hadn't thought about (and hence not tested) a structure like 2M8Z...

The problem with what you tried to do is that the option "-dnatype ds" assumes the pdb file to have to two strands. And your structure has just one though it forms a helical structure.

You could make a CG topology without elastic network using option "-dnatype ss" but that won't be stable for such a structure. I added a new option to the script "-dnatype stiff-ss" that is a stiff elastic network and will retain the crystal structure. If you go back to http://cgmartini.nl/cgmartini/index.php/309-martini-dna-beta there is a version 2 of the beta with the updated martinize-dna.py that has this option.

Let me know how it goes.
- Jaakko
Last edit: 5 years 2 months ago by jaakko.

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5 years 1 month ago #3621 by Bryan
Replied by Bryan on topic Building CG DNA using martinize-dna.py
hi jaakko,

I am looking to simulate RNA/protein systems. Have you ever considered to build one for cg RNA?
I am happy to test!

Bryan

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5 years 1 month ago #3622 by jaakko
Replied by jaakko on topic Building CG DNA using martinize-dna.py
Hi Bryan,

extending the model to RNA is in the plans but will take a while before we get there. I'll keep you updated here how this progresses.

- Jaakko

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