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Membrane builder not making correct thickness
#37826 04/07/20 05:58 PM
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Hi, I am new to using CHARMM-GUI and seek to prepare a system with an ion channel in a lipid bilayer for studies of ion permeation.

My problem is this:
After taking my PDB file and preparing it for Step 1 in membrane builder, I noticed that there is no input to actually change the thickness dimension of the hypothetical membrane with which to build in the membrane in during later steps. It seems the program just uses Z= +20 and Z= -20 angstroms automatically. However, there are clearly portions of my TM helices which are not covered by the the plane of this thickness, and even if I adjusted the Z position to center the planes more they still wouldn't cover it. Further, because of this, it appears to not adequately solvate the TM regions either.

These are my questions:
Is there a way to adjust this thickness parameter? Does it actually matter (eg. does the program actually adjust this when the membrane is built in for later steps)? Once I solvate the entire system can it add waters to some of the pore regions not covered by Step 1?

I looked around on the forums and guides and I didn't see stuff about this topic, but if I am mistaken please point me in the right direction! Any help would be appreciated smile

*Note, it looks like the attachment manager on the site doesn't work, so I would have uploaded pictures to show what I am talking about but unfortunately can't. I could perhaps message them to someone if looking at them would help.

Re: Membrane builder not making correct thickness
themosterik #37828 04/07/20 06:24 PM
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In principle, the thickness ought to be a function of the lipids requested; which ones are you using?

BTW, there is a specific forum for CHARMM-GUI related questions, further down on the main page; did you not look through the READ BEFORE POSTING topic?

Last edited by rmv; 04/07/20 06:30 PM. Reason: forum usage

Rick Venable
computational chemist

Re: Membrane builder not making correct thickness
rmv #37833 04/09/20 10:36 PM
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Hi Rick,
Thank you for the quick response! I must admit I did read it but clearly not carefully enough! My apologies.

My plan is to use whichever lipid length covers the TM helices most completely; other than that I didn't have a strong preference other than it being something typically in a eukaryotic membrane.

The plane that is built in Step 1 already does not cover the the TM helices; when the program builds in the membrane in later steps, is it not constrained to the plane that is drawn in step 1? So, it could build the bilayer past the initial plane that is drawn, or will it attempt to pack it all in there?

Re: Membrane builder not making correct thickness
themosterik #37834 04/10/20 12:40 PM
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Just want to say; that I have performed the actual building of the membrane with varying tail lengths (14C and 18C) and the program doesn't constrain building the bilayer and energy minimizing in a way that constrains the bilayer to the originally drawn plane. I think it uses that the plane simply as a way to obtain the correct orientation for the bilayer, but it doesn't seem to use it as a 'box' in which to build. Could be wrong but that's what it seems like.

Re: Membrane builder not making correct thickness
themosterik #37835 04/10/20 04:32 PM
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Most PC lipids up to C18 typically have P:P distances across the bilayer of 40 Å or less in the fluid phase, which is an overestimate for e.g. DMPC. To get thicker membranes you probably need some PE lipids, which pack tighter and lead to thicker chain regions. An alternative might be to use longer chains. The choices here should be justified by the lipid composition of the system under study.

Finally, there can be adaption, in that over time a TM helix might tilt to adapt to the hydrophobic thickness, the membrane might thicken around the TM helix, or some combination of these two. You may need to run the simulation for a while (a few hundred ns) to see that happen.

I don't know enough of the details and cannot answer specific questions about how CHARMM-GUI works, so I suggest posting to that forum, and/or perhaps obtaining and reading the CHARMM-GUI citations.

Last edited by rmv; 04/10/20 04:39 PM.

Rick Venable
computational chemist


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