normal is this normal

  • Tarsis G Ferreira
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2 years 9 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

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2 years 9 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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2 years 9 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

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2 years 9 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.

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