normal How to fix martinize.py error?

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2 years 10 months ago #9149 by human369
How to fix martinize.py error? was created by human369
Hello.
I just tried this command but it didn't work with this error.

<command>
python martinize.py -f edit2.gro -o cg.top -x relax.pdb -p Backbone -ff martini22_ff.py


<error meassage>
File "martinize.py", line 1851, in <module>
forcefields += [ff[:-3] for ff in os.listdir(os.environ["GMXDATA"]+"/top/") if ff[-6:] == "_ff.py"]
OSError: [Errno 2] No such file or directory: '/apps/applications/GROMACS/2020.2/intel/19.0.5/impi/19.0.5/mic-knl/share/top/'

How can I fix? Pleas let me know it.

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2 years 10 months ago #9150 by bart
Replied by bart on topic How to fix martinize.py error?
Remove the .py in the force field file specification

python martinize.py -f edit2.gro -o cg.top -x relax.pdb -p Backbone -ff martini22_ff

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2 years 10 months ago #9151 by human369
Replied by human369 on topic How to fix martinize.py error?
Thank you for your answering
By the way, I have the same problem with the command.
(python martinize.py -f edit2.gro -o cg.top -x relax.pdb -p Backbone -ff martini22_ff)
I downloaded the "martini22_ff.py" from Github.
Should I put this file somewhere?

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2 years 9 months ago - 2 years 9 months ago #9152 by bart
Replied by bart on topic How to fix martinize.py error?
Take a look at the martini2 protein tutorial. You ares still getting the -ff flag wrong. Also you might want to use dssp for the secondary structure prediction. Here is a link to the tutorial:
protein tutorial martini 2

tutorial instruction:
python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -ss <YOUR FILE> -p backbone -ff martini22

and your line then becomes:
python martinize.py -f edit2.gro -o cg.top -x relax.pdb -p Backbone -ff martini22

I think it might also be needed to run martinize with python2 but I am not 100% certain about this. Just in case you see weird print statement related errors use:
python2 martinize.py -f edit2.gro -o cg.top -x relax.pdb -p Backbone -ff martini22

Cheers,

Bart
Last edit: 2 years 9 months ago by bart.

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2 years 9 months ago #9154 by human369
Replied by human369 on topic How to fix martinize.py error?
Thank you for your kindness!

I will try

Have a good day.

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