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how to embed a protein into a bilayer membrane?
- fugui
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10 years 11 months ago #1556
by fugui
how to embed a protein into a bilayer membrane? was created by fugui
Hello everyone:
I hope to study a membrane protein using coarse grained MD. There is some kines of membrane here:
md.chem.rug.nl/cgmartini/index.php/downl...example-applications
I can construct a protein-membrane complex using the method here:
www.bevanlab.biochem.vt.edu/Pages/Person...ls/membrane_protein/
but i do not know how to construct a protein-memebrane complex using the CG membrane although i can do it using an all-atomic force field.
Could anyone give me some suggestion on that?
Any suggestion is appreciated.
Fugui
I hope to study a membrane protein using coarse grained MD. There is some kines of membrane here:
md.chem.rug.nl/cgmartini/index.php/downl...example-applications
I can construct a protein-membrane complex using the method here:
www.bevanlab.biochem.vt.edu/Pages/Person...ls/membrane_protein/
but i do not know how to construct a protein-memebrane complex using the CG membrane although i can do it using an all-atomic force field.
Could anyone give me some suggestion on that?
Any suggestion is appreciated.
Fugui
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10 years 11 months ago #1557
by djurre
Replied by djurre on topic how to embed a protein into a bilayer membrane?
Did you try to use g_membed? I think it should also work for Martini (but I never tried).
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- fugui
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10 years 11 months ago #1559
by fugui
Replied by fugui on topic how to embed a protein into a bilayer membrane?
Thanks.
But another problem is that we cannot retransform the coarse-grained lipid into all-atom structure.
But another problem is that we cannot retransform the coarse-grained lipid into all-atom structure.
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10 years 11 months ago #1560
by djurre
There is a tutorial on that (reverse transformation).
Replied by djurre on topic how to embed a protein into a bilayer membrane?
Does that mean it worked?fugui wrote: Thanks.
fugui wrote: But another problem is that we cannot retransform the coarse-grained lipid into all-atom structure.
There is a tutorial on that (reverse transformation).
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- fugui
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10 years 11 months ago #1561
by fugui
Replied by fugui on topic how to embed a protein into a bilayer membrane?
Sorry, i did not try.
I am going to use NAMD to do coarse MD because it seems that it is easier using VMD. In addition, there is a good tutorial.
www.ks.uiuc.edu/Training/Tutorials/spect...dex.html#coarsegrain
I am going to use NAMD to do coarse MD because it seems that it is easier using VMD. In addition, there is a good tutorial.
www.ks.uiuc.edu/Training/Tutorials/spect...dex.html#coarsegrain
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10 years 11 months ago #1562
by djurre
Replied by djurre on topic how to embed a protein into a bilayer membrane?
VMD indeed is pretty easy because of it's graphical user interface. I hope you get things to work!
Just out of curiosity: do you like the VMD tutorial better then the one on this page? If so, what is better? (knowing this might enable us to improve on ours!) Thank you.
Just out of curiosity: do you like the VMD tutorial better then the one on this page? If so, what is better? (knowing this might enable us to improve on ours!) Thank you.
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10 years 11 months ago #1563
by fugui
Replied by fugui on topic how to embed a protein into a bilayer membrane?
I think the tutorials of VMD are better because every step is very clear, and i can know each detail of the simulation.
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