unanswered Martini error Keyerror B + ds-RNA

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2 months 2 weeks ago - 2 months 2 weeks ago #9214 by mandar
Martini error Keyerror B + ds-RNA was created by mandar
Hi,
I am building the MARTINI CG model using 1410 nucleotide long RNA. It has multiple helix parts and loops and a single chain.
1. To avoid the unwinding of such a large RNA structure, I am trying to use the ds-soft approach.
2. As there is only one chain, I am getting a "Keyerror: B" error as discussed earlier.

Martinize_nucleotide.py script options are:
python martinize-nucleotide.py -type ds-soft -f gmx-rna.gro -o cg-rna.top -x cg-rna.pdb

Is it possible to model RNA with the ds-soft approach? or SS is only a possible martinize option in this case?

Thanks in advance.

Best,
Mandar Kulkarni
Last edit: 2 months 2 weeks ago by mandar. Reason: Added command whch was used to generate structure.

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