Building Gramicidin A
Add Water
Here is where we combine our protein and lipid components with water to form a complete biomolecular system.
The first stage is to combine the protein, lipid, and water into a single pdb and psf file. For the water we use a pre-equilibrated block of water.
There is a bug in the solvate 1.1, included with VMD 1.7.1 and 1.7.2,
that results in extra angle terms being generated for water molecules when
solvate is run after another topology file is loaded into psfgen. This
can be avoided by running the water generation step in a separate VMD
(which is, unforunately, incompatible with the web format of this
tutorial, and therefore the bug was present in this example).
This is fixed in solvate 1.2, with future versions of VMD.
As a workaround, this tutorial temporarily downloads solvate 1.1.1, which
works correctly but does not require the newer version of psfgen used by
solvate 1.2. You may download and install this plugin permanently by
downloading and unpacking one of
solvate-1-1-1.tar.gz or
solvate-1-1-1.zip or
in VMD's plugins/noarch/tcl directory.
Run this step! Continue
add_water.vmd # STEP 5: Add Water resetpsf # Read in structure files readpsf protein.psf readpsf pope.psf # Read in coordinates coordpdb protein_move.pdb coordpdb pope_move.pdb writepsf pope_gram.psf writepdb pope_gram.pdb resetpsf # solvate 1.1 has a bug, either 1.1.1 (downloaded) or 1.2 will work package require solvate 1.1.1 solvate pope_gram.psf pope_gram.pdb \ -o pope_gram_wat -s WT -b 2.4 -t 5 -z 15 +z 15 mol delete all mol load psf pope_gram_wat.psf pdb pope_gram_wat.pdb
