normal Insane.py protein location away away from membrane

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2 years 8 months ago #9227 by yanhua
Is there a command in insane which allows for the insertion of a protein away from the membrane rather than inside the membrane?

The -dm flag seems to only allow for moving the protein a certain amount from the membrane but not outside the membrane. Would it be possible to put the membrane away from the membrane i.e. 5 nm from the membrane?

Thx!

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2 years 8 months ago #9228 by vainikka
I don't think insane comes with this functionality, but what you could try is to set up a bilayer with insane (make sure you make the box large enough) and the use gmx insert-molecules to place the protein where you want. Use the -ip flag, see manual.gromacs.org/current/onlinehelp/gmx-insert-molecules.html for more details.

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2 years 8 months ago #9230 by tsjerk
The -dm flag sets the difference from the center of the membrane. The thickness of a membrane is approximately 4 nm, so setting -dm 7 should position the protein 5 nm above the membrane. Now you probably also want to have the protein 5 nm away from the other side, so you probably will want to set the height of the box manually with -z.

Cheers,

Tsjerk

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2 years 8 months ago #9231 by tsjerk
It does!

T.

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2 years 8 months ago #9232 by yanhua
I only managed to use the -dm flag till a certain number i.e. 5 but as soon as it goes out of the membrane i.e. -dm 7 I get the following error:

; The protein seems not to be inside the membrane.
; Run with -orient to put it in.
Traceback (most recent call last):
File "./insane/__main__.py", line 10, in <module>
File "./insane/insane/cli.py", line 145, in main
File "./insane/insane/core.py", line 1175, in old_main
File "./insane/insane/core.py", line 834, in setup_membrane
ZeroDivisionError: float division by zero

Did you manage to put the protein outside the membrane without invoking an errror?

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