1. In a Terminal window in your 4_combine directory, copy the input files that you have created while working on the previous sections, using the following commands:
cp ../1_build_cg_model/cg_monomer.pdb .
cp ../1_build_cg_model/cg_monomer-2.pdb .
cp ../1_build_cg_model/cg_monomer.top .
cp ../3_cg_membrane/mixture.pdb .
cp ../3_cg_membrane/lipid-ion.top .
The last input files needed is a pdb of ions, ions.pdb, which is located at your current directory 4_combine/example-input.
2. Start VMD and in the VMD Tk Console window, type the following command:
This command calls the script build.tcl, which will replicate six copies of BAR domain dimers and combine the BAR domains, lipids and ions together.
3. The output of the script build.tcl will be a psf file (6bar.psf) and a pdb file 6bar.pdb containing six BAR domain dimers on top of a membrane patch, neutralized by ions.
4. Take a look at the build.tcl.
This script contains the following steps: (1) Load the two monomers of a BAR domain dimer. (2) Move the monomers to appropriate locations, to form a lattice. (3) Call VMD plugin psfgen and input SBCG topology files for BAR domains, lipids and ions. (4) Input coordinates of the six BAR domain dimers, lipid membrane, and ions. (5) Generate psf and pdb files for the combined system. More detailed descriptions of the commands are included in build.tcl as comments beginning with ``#''. You can view the commands and comments in build.tcl using any text editor, or, e.g., using ls command in the VMD Tk Console.
5. Load the output system into VMD using the following command in the Tk Console:
mol load psf 6bar.psf pdb 6bar.pdb
6. Measure the center and dimension of the system by following commands:
set sel [atomselect top all]
measure center $sel
measure minmax $sel
Record the above values for use in the next section.