.. _example mper-tm symmetric bilayer: Example 16: HIV-1 Env MPER-TM Trimer in a DMPC Symmetric Bilayer -------------------------------------------------------------------------- .. figure:: my_6e8w_pc.png HIV-1 gp41 (MPER-TM) trimer embedded in a DMPC lipid bilayer. Each protein chain is colored uniquely, and a transparent isodensity surface is shown. Waters and counterions are not shown. `PDB ID 6e8w `_ is a trimeric HIV-1 Env gp41 construct embedded in a DMPC lipid bilayer (the authors also mention DHPC, but these are detergents that don't readily form bilayers). The structure was determined by NMR, and the structure file contains 15 models, and no lipids are included in the file. This example shows how to use ``pestifer`` to generate a membrane-embedded protein system from this structure. .. literalinclude:: ../../../../pestifer/resources/examples/ex16/inputs/hiv-mpertm3-membrane1.yaml :language: yaml .. task-table:: ../../../../pestifer/resources/examples/ex16/inputs/hiv-mpertm3-membrane1.yaml Notice first that packmol's path is set explicitly in the ``paths`` section to ``/usr/local/bin/packmol``. This avoids any version of packmol that may be installed via conda; for example, when a user installs AmberTools via conda, packmol is installed as a dependency, but this version of packmol is not compatible with the current version of ``pestifer``. If packmol is not found at the specified path, the membrane-building process will fail. The key task in this example is the ``make_membrane_system`` task. This task specifies a ``bilayer`` subtask and an ``embed`` subtask. The ``bilayer`` subtask specifies the composition of the two leaflets, directives for using ``packmol`` to assemble the initial *minimal* bilayer patch, and relaxation protocols for relaxing the patch and the full-sized bilayer, prior to embedding the protein. The ``embed`` subtask specifies how the protein is to be oriented and placed in the bilayer. Immediately following the ``make_membrane_system`` task, the ``minimize`` task is used to relax the system after embedding the protein. This is then followed by a series of ``md`` tasks to progressively equilibrate the system density and the bilayer area. A detailed explanation of the two subtasks can be found at :ref:`subs_buildtasks_make_membrane_system`. Results +++++++ The plots below are generated by default during the membrane-building process. .. figure:: 15-patch-a_x-b_y-c_z.png Cell dimensions vs time step for the initial 200-lipid bilayer patch. .. figure:: 15-patch-density.png System density vs time step for the initial 200-lipid bilayer patch. .. figure:: 15-patch-pressureprofile.png Pressure profiles for selected time intervals during the patch relaxation. The ``mdplot`` task generated the following plots for the membrane-embedded system. .. figure:: 15-bilayer-a_x-b_y-c_z.png Cell dimensions vs time step for the protein-embedded membrane. .. figure:: 15-bilayer-density.png System density vs time step for the protein-embedded membrane. .. figure:: 15-bilayer-pressureprofile.png Pressure profiles for selected time intervals during the protein-embedded membrane relaxation. .. raw:: html

Example author: Cameron F. Abrams     Contact: cfa22@drexel.edu