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Martini tutorials: DNA
- ChristinaL
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6 years 11 months ago #7279
by ChristinaL
Martini tutorials: DNA was created by ChristinaL
Hi there.
I'm doing the DNA Martini tutorial. I am using the martinize-dna.py script. I have used it on the provided .pdb file, to see how it works. I works fine, but when I use my own .pdb file for my project I get the error: ValueError: chr() arg not in range(256). I looked online, and the solution appeared to be running the script using python2. I tried this, and this does not work for either the provided .pdb file or my own .pdb file. It gives the error message: Forcefield 'elnedyn22dna' can not be found. I can see from the script that is uses both martini22dna and elnedyn22dna, and while the first one is provided, I can't find the second one. I have looked everywhere online, with no result. On your site I found ElNeDyn2.1, but this does not work. Is there a way to get the correct force field, or is there another workaround, that might work?
- Christina L.
I'm doing the DNA Martini tutorial. I am using the martinize-dna.py script. I have used it on the provided .pdb file, to see how it works. I works fine, but when I use my own .pdb file for my project I get the error: ValueError: chr() arg not in range(256). I looked online, and the solution appeared to be running the script using python2. I tried this, and this does not work for either the provided .pdb file or my own .pdb file. It gives the error message: Forcefield 'elnedyn22dna' can not be found. I can see from the script that is uses both martini22dna and elnedyn22dna, and while the first one is provided, I can't find the second one. I have looked everywhere online, with no result. On your site I found ElNeDyn2.1, but this does not work. Is there a way to get the correct force field, or is there another workaround, that might work?
- Christina L.
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- Abhi
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3 years 1 month ago #8891
by Abhi
Replied by Abhi on topic Martini tutorials: DNA
Hi did you find any answer? I want to do MD simulations for ssDNA which is an Aptamer. which force field should I use ? and how do I create topology for it?
Thanks
Abhi
Thanks
Abhi
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- israini
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1 year 2 weeks ago #9604
by israini
Replied by israini on topic Martini tutorials: DNA
Hi,I have faced the same problem,
the solution is you should change the environtment python to python2 instead python3 because the script only can run with python2
I hope ot can helps
the solution is you should change the environtment python to python2 instead python3 because the script only can run with python2
I hope ot can helps
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