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is this normal
- Tarsis G Ferreira
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2 years 6 months ago #9187
by Tarsis G Ferreira
is this normal was created by Tarsis G Ferreira
Dear users/developers,
I have just used insane to embed my two proteins in POPC.
Proteins topology are alright, but I see this empty space between them.
Is this normal and will be repacked or I am missing something?
image
I have just used insane to embed my two proteins in POPC.
Proteins topology are alright, but I see this empty space between them.
Is this normal and will be repacked or I am missing something?
image
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- vainikka
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2 years 6 months ago #9189
by vainikka
Replied by vainikka on topic is this normal
By the looks of it, you have a large bilayer. Unless you have a very specific reason for having a certain amount lipids/protein, I doubt it will matter as the bilayer will contract almost instantly during equilibration.
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- tsjerk
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2 years 6 months ago #9190
by tsjerk
Replied by tsjerk on topic is this normal
Hi Tarsis,
Add the option -ring to your command line.
That is a bit of an oddity; the default for proteins was to exclude the inner space from placement of lipids, to embed pore forming structures. The -ring option was added to allow placing lipids inside ring like structures. The same is needed for separated proteins, but the option was not renamed.
Cheers,
Tsjerk
Add the option -ring to your command line.
That is a bit of an oddity; the default for proteins was to exclude the inner space from placement of lipids, to embed pore forming structures. The -ring option was added to allow placing lipids inside ring like structures. The same is needed for separated proteins, but the option was not renamed.
Cheers,
Tsjerk
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- Tarsis G Ferreira
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2 years 6 months ago #9191
by Tarsis G Ferreira
Replied by Tarsis G Ferreira on topic is this normal
Thanks Tsjerk,
I initially had 5 proteins to embed on that membrane, just reduced to 2 to troubleshoot. that's why the membrane size.
Many thanks -ring worked.
I initially had 5 proteins to embed on that membrane, just reduced to 2 to troubleshoot. that's why the membrane size.
Many thanks -ring worked.
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