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tutorial problem (protein in water)
- echo0347
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11 years 2 months ago #1406
by echo0347
tutorial problem (protein in water) was created by echo0347
i try to do the "protein in water" exercise as tutorial. (The version of my python is 2.7.3.)
When I try "./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp -p backbone",
the screen shows:
"Traceback (most recent call last):
File "./martinize.py", line 5101, in <module>
options = option_parser(args,options,lists,version)
File "./martinize.py", line 381, in option_parser
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: 'backbone'"
This is my first time to use MARTINI. Can you tell me what is the problem? How to deal with it?
When I try "./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp -p backbone",
the screen shows:
"Traceback (most recent call last):
File "./martinize.py", line 5101, in <module>
options = option_parser(args,options,lists,version)
File "./martinize.py", line 381, in option_parser
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: 'backbone'"
This is my first time to use MARTINI. Can you tell me what is the problem? How to deal with it?
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- nivedita
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10 years 7 months ago #1946
by nivedita
Replied by nivedita on topic tutorial problem (protein in water)
hi,
when you run martini script before that you have use dssp program to convert .pdb file into .dssp or .ssd format (secondary structure format) then only you can use martini script whatever you wrote just include -dssp filename.dssp.
when you run martini script before that you have use dssp program to convert .pdb file into .dssp or .ssd format (secondary structure format) then only you can use martini script whatever you wrote just include -dssp filename.dssp.
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- djurre
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10 years 7 months ago #1948
by djurre
Replied by djurre on topic tutorial problem (protein in water)
Right. So the correct command would be:
./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /where/ever/your/dssp/program.is -p backbone
./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /where/ever/your/dssp/program.is -p backbone
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