- Posts: 2
Insane.py protein location away away from membrane
- yanhua
-
Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 5 months ago #9227
by yanhua
Insane.py protein location away away from membrane was created 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!
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!
Please Log in or Create an account to join the conversation.
- vainikka
-
- Offline
- Admin
Less
More
- Posts: 91
2 years 5 months ago #9228
by vainikka
Replied by vainikka on topic Insane.py protein location away away from membrane
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.
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
2 years 5 months ago #9230
by tsjerk
Replied by tsjerk on topic Insane.py protein location away away from membrane
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
Cheers,
Tsjerk
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
2 years 5 months ago #9231
by tsjerk
Replied by tsjerk on topic Insane.py protein location away away from membrane
It does!
T.
T.
Please Log in or Create an account to join the conversation.
- yanhua
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 2
2 years 5 months ago #9232
by yanhua
Replied by yanhua on topic Insane.py protein location away away from membrane
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?
; 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?
Please Log in or Create an account to join the conversation.
Time to create page: 0.095 seconds