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!
the rpoblem was solved with a hybrid tutorial (KALP and https://training.vi-seem.eu/images/trainingMaterial/LifeSciences/memprot_tutorial.pdf):
instead of membrane builder -> genconf -nbox (to enlarge the XY plane of bilayer);
minimization of this system - slightly changed em.mdp from KALP;
a new vectors set to gro (parallelepiped -> cube)
genbox added water into the cubic box
minimization + equilibration of the system again and alignment of the protein to the center of the system with translation along the Z axis to catch the correct immersion;
nfaltedgro method -> g_membed for protein embbeding (a long process)
subsequent steps of minimization and equilibration with nose- hoover thermostat (but ut seems it doesn't work with a leapfrog integrator), semiisotropic pcoupletype and MD.
everything is fine, however in the case the protein structure should be almost excelent, without clashes and so on....
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