normal martinize-dna.py error

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2 months 4 days ago #8577 by jfliu21
martinize-dna.py error was created by jfliu21
Hello, I'm a beginner, and trying to use Martini on a DNA origami with ~7000 bp. when I try "python martinize-dna.py -dnatype ds-stiff -f DNA-cleaned.gro -o cg-dna.top -x cg-dna.pdb"

File "martinize-dna.py", line 4522, in main
chains = [ Chain(options,residuelist[i:j],name=chr(65+k)) for i,j,k in chains ]
ValueError: chr() arg not in range(256)

I searched the error via google, found that python3 will be okay. I'm wondering do you have a python3 version of martinize-dna.py? I can only find python3 version of martinize.py in your website.

BTW, whether Martini is suitable for the 7000 bp DNA origami MD simulation?

Many thanks.

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2 months 4 days ago #8578 by vainikka
Replied by vainikka on topic martinize-dna.py error
Hi,

Somebody else ran in to the same problem back in 2015, check out:
md.chem.rug.nl/index.php/component/kunen...850-martinize-dna-py

One of the users solved their similar problem by increasing the cut-off:

"The cut_off range was way to low for my system creating a huge number of chains in my case. The reason I needed a high cut off range up to 100.0 was because of the multiple convertion of the sequence for the origami creating large bond distances."

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