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how to use martinize.py ？
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12 years 6 months ago #813
by 55
how to use martinize.py ？ was created by 55
I'm new here.
Can you help me? please!
Morning,I use:
./martinize.py -f 1UBQ.pdb -o system.top -x cg 1UBQ.pdb -dssp /wherever/dsspcmbi -p backbone
Get:
Traceback (most recent call last):
File "./martinize.py", line 21, in ?
import subprocess as subp
ImportError: No module named subprocess
So,what should I do ? In order to generate both a structure and a topology by martinize.py
Thanks so much!
Can you help me? please!
Morning,I use:
./martinize.py -f 1UBQ.pdb -o system.top -x cg 1UBQ.pdb -dssp /wherever/dsspcmbi -p backbone
Get:
Traceback (most recent call last):
File "./martinize.py", line 21, in ?
import subprocess as subp
ImportError: No module named subprocess
So,what should I do ? In order to generate both a structure and a topology by martinize.py
Thanks so much!
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- djurre
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12 years 6 months ago #816
by djurre
Replied by djurre on topic how to use martinize.py ？
Dear GaoBo Yu,
There are probably two (or even more) things going wrong.
First, there was a typo in the tutorial, which now is also in you command: instead of "cg 1UBQ" it should read "cg_1UBQ". I changed it in the tutorial.
Second, the python module subprocess seems to be not installed. As this is, as far as I know, a standard module these days, I think you might have an old version of python. You could check by starting python (type 'python' on the commandline). If the version is older than 2.6.x you probably want to update python, for example to 2.7 (not 3.0!).
Groetnis,
Djurre
There are probably two (or even more) things going wrong.
First, there was a typo in the tutorial, which now is also in you command: instead of "cg 1UBQ" it should read "cg_1UBQ". I changed it in the tutorial.
Second, the python module subprocess seems to be not installed. As this is, as far as I know, a standard module these days, I think you might have an old version of python. You could check by starting python (type 'python' on the commandline). If the version is older than 2.6.x you probably want to update python, for example to 2.7 (not 3.0!).
Groetnis,
Djurre
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- wajii
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8 years 1 month ago #5395
by wajii
Replied by wajii on topic how to use martinize.py ？
hi
iam new here
currently working on CG simmulation of Prion protein
i am facing the same problem
of martinize.py
cant proceed it
can anyone help me
iam new here
currently working on CG simmulation of Prion protein
i am facing the same problem
of martinize.py
cant proceed it
can anyone help me
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- peterkroon
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8 years 1 month ago #5408
by peterkroon
Replied by peterkroon on topic how to use martinize.py ？
Please provide the precise commands you used and their output. Otherwise we can't tell what's going wrong either.
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