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Building CG DNA using martinize-dna.py
- doa.hawamdeh
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10 years 4 weeks 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'
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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- jaakko
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10 years 4 weeks ago - 10 years 4 weeks 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
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: 10 years 4 weeks ago by jaakko.
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- Bryan
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10 years 3 weeks 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
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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- jaakko
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10 years 3 weeks 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
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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- GhazalehYA
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4 years 2 months ago #8437
by GhazalehYA
Replied by GhazalehYA on topic Building CG DNA using martinize-dna.py
Hello,
I have the same problem, I'm trying to build the coarse grained RNA using martinize-nucleotide.py. I have using RNA with one strands. Could you please help with martinize-nucleotide.py script?
Traceback (most recent call last):
File "martinize-nucleotide.py", line 5023, in <module>
main(options)
File "martinize-nucleotide.py", line 4529, in main
order, merge = check_merge(chains, options, options, options and options)
File "martinize-nucleotide.py", line 2720, in check_merge
merges = [[(i.isdigit() and int(i) or dct+1)-1 for i in j] for j in m_list]
KeyError: 'B'
Thank you,
Gazel
I have the same problem, I'm trying to build the coarse grained RNA using martinize-nucleotide.py. I have using RNA with one strands. Could you please help with martinize-nucleotide.py script?
Traceback (most recent call last):
File "martinize-nucleotide.py", line 5023, in <module>
main(options)
File "martinize-nucleotide.py", line 4529, in main
order, merge = check_merge(chains, options, options, options and options)
File "martinize-nucleotide.py", line 2720, in check_merge
merges = [[(i.isdigit() and int(i) or dct+1)-1 for i in j] for j in m_list]
KeyError: 'B'
Thank you,
Gazel
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