[gmx-users] Fwd: ion channel in lipid bilayer

Kroon, P.C. p.c.kroon at rug.nl
Mon Feb 19 00:51:06 CET 2018

Hi Alex,

Try either insane.py, or charmm-gui. I can't provide links, since I'm on my

You may need to generate the topology (itp) of the protein, which you can
do with calling pdb2gmx on just the protein. You should have a topology
(itp) of your favourite lipid.


On 18 Feb 2018 13:54, "alex rayevsky" <rayevsky85 at gmail.com> wrote:

> I'm sorry for repeat, but nobody answered the question and I decided to
> duplicate the request. Maybe it is a problem with a form of question or its
> content, please, point me the mistake.
> Hi all!
> I have a question concerning immersion of the ion channel (four subunits
> with extracellular domains and a bundles of helixes)  into the lipid
> bilayer. 6 years ago I used some tutorial or mailing lists, which described
> the way from KALP15 tutor. With CCR5 model there were no problems at all.
> Now I have a not 'cylindric'  protein with a complex shape and overhanging
> domains.
> the forcefield is CHARMM36, lipid type - POPG.
> I tried Membrane builder, but couldn't orient the plane of the membrane by
> changing XYZ principles many times in different combinations.. Thus I used
> a slightly modified KALP15 method (other .itps, lipids and water
> molecules).  First of all after pdb2gmx for protein a series of topologies
> were generated with identifiers in the name, as it was assigned in each
> chain. However editconf produced a new pdb from the outpu gro without any
> ID or terminators for the chains, in Pymol it is represented with a
> tetramer entirely highlithing if a single chain is selected (maybe it is a
> reason of faults at later stages).
> Well, it works fine until the perl script execution. Beside some problems
> with the output (system_inflated.gro was corrupted, but I repaired it with
> simple python scripting and got a pretty protein in the center of rare
> molecules, which looks reliable enough) I started to compact the bilayer to
> rich the lipid area of ~53A^2. I finished it on the 13 stage of perl
> execution - the distance between nearest lipids was about 16A, however, the
> layer was really holey. At the same time the protein was not surrounded
> from all sides. But if I try to put lipids closely one to other, they are
> simultaneously penetrate the protein body.
> Is it the correct method for such kind of simmulations? Could I increase
> the number of POPG molecules after getting inflated.gro file with scaled up
> bilayer (the initial step for tightning) before scaling iterations? I can
> do it manually by copy of the layer (all lipid coordinates) and its
> rotation around Y axis in any soft to enlarge the number of molecules in
> the cell (even 200 mols is more than 128). Of course I will make changes in
> a topology file. It seems, that I will obtain a fully wrapped protein
> without anxiety about clashes or presure in cavities...
> What do You think? Thank You in advance!
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