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normal Secondary structure input for martinize.py

  • joshcarr
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8 years 11 months ago #4564 by joshcarr
Secondary structure input for martinize.py was created by joshcarr
Hello,

I am attempting to use martinize.py to build a Martini model for my system (a membrane protein). I had some issues using the GROMACS program do_dssp on my cluster, so instead I simply downloaded DSSP and ran that executable directly on my system. However, I'm stuck because I can't tell what the appropriate input syntax for martinize.py is. It's stated ( here ) that I should either use the GROMACS ssdump format--which I don't know and cannot find an example of online (is this the same as the DSSP output?)--or a string--but the proper format for the string is not given. Could someone please let me know the best way for me to feed input to martinize.py?

Thanks,

Josh

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8 years 11 months ago #4566 by tsjerk
Replied by tsjerk on topic Secondary structure input for martinize.py
You can pass the DSSP executable as argument to martinize, with the option -dssp
Otherwise, you should be able to give the file with dssp output as argument to -ss

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8 years 11 months ago #4567 by joshcarr
Replied by joshcarr on topic Secondary structure input for martinize.py
Great. I expected something like that might be the case but wanted to make sure.

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