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
*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.