Dear all,
Hi. I would like to do simulation for my full protein model (including transmembrane domain) extracted from Cryo-EM reported pdb file. I have used Orientations of Proteins in Membranes (OPM) database for setting the orientation of TMD in my model and the hydrocarbon core of the lipid bilayer then used the processed .pdb file as input for implicit solvent model by CHARMM-GUI. I have also prepared the explicit model and done some simulation for both models. The implicit solvent model starts breaking in some of alpha helices in TMD part and also in protein binding domain as well. Having closed look into the axis in the origin position for explicit and implicit models (attached picture) shows that the orientation of lipid bilayer in membrane domain is not correctly has been set in implicit model compare to explicit model (the explicit model passed smoothly simulation step so far). So I am wondering how to set the lipid bilayer and membrane orientation in implicit model same as explicit one. They both were prepared using same starting pdb file taken from OPM webserver.
Any suggestion/help will be appreciated.
Bests
Zahra
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