GBSW Tutorial

Objective and Overview

The objective of this tutorial is to introduce users to the GBSW implicit solvent model in CHARMM. GBSW stands for a generalized Born (GB) model with a simple smoothed SWitching function. In this tutorial we will:

  • Generate the pentameric phospholamban by reading PDB:1ZLL into CHARMM, and orient its transmembrane (TM) domain along Z,
  • Solvate the protein with GBSW implicit solvent
  • Minimize, equilibrate, and simulate the system with and without membrane
  • use 5-fold symmetry in the membrane simulation
Phospholamban is a transmembrane (TM) protein which regulates Ca2+ ATPase. The number of simulation steps is limited in this tutorial due to the time constraint, but can be extended to explore the stability and dynamics of the protein in solution as well as in membrane environment.

Please note that CHARMM supports various implicit membrane models such as IMM1, GB/IM, and GBMV. (Note, to run this tutorial you need to download and unpack the pdb subdirectory and the parameters. You can also download the output files if you wish to check yourself.)

A molecular graphical view of pentameric phospholamban in GBSW membrane implicit solvent model.

GBSW simulations with phospholamban (PDB:1ZLL)

gbswmemb1.inp This input illustrates a typical setup for simulations in GBSW membrane without images. In this example, we will
  1. Read the coordinates of each monomer by generating their PSF in CHARMM.
  2. Orient the TM domains along Z and adjust their position to place in the hydrophobic core

    coor stat
    coor orient
    coor stat
    coor rotate ydir 1.0 phi 90.0
    coor trans zdir -?zmin
    coor trans zdir -17.0

  3. Read GBSW optimal radii

    prnlev 0
    stream radii_prot_na.str
    stream radius_gbsw.str
    prnlev 5 node 0
    define check select (.not type H* ) .and. -
    ( property wmain .eq. 0.0 ) show end
    if ?nsel ne 0 stop !some heavy atom have a zero radius

  4. Setup GBSW

    gbsw sgamma 0.005 nang 50 dgp 1.5 tmemb 30.0 msw 2.5

    where sgamma is the surface tension coefficient, nang is the number of angular integration points, dgp is a grid spacing for lookup table, msw is the half of switching length over which hydrophobic environment is changed to solvent region, and tmemb-msw*2 is the hydrophobic length of the membrane, i.e., here it is 25 A.

  5. Minimize, equilibrate, and let it go for sampling. One can certainly extend the simulation by simply changing the number of simulation steps or restarting it. Once the calculation is done, one can see the dynamics of the protein using "vmd".

gbswmemb2.inp This input illustrates a typical setup for simulations in GBSW membrane with images. In this example, we will use 5-fold symmetry along Z. Once we read and orient all the five monomers as illustrated in "gbswmemb1.inp", we will  delete all the monomer except the first one;

delete atom sele .not. segid PROA end

The 5-fold symmetry is setup;

* 5-fold symmetry

ROTATE 0.0 0.0 1.0  72.0

ROTATE 0.0 0.0 1.0 144.0

ROTATE 0.0 0.0 1.0 216.0

ROTATE 0.0 0.0 1.0 288.0


So, we only simulate one monomer, but there are interactions with others (images) under the constraint of the symmetry. One has to put the "image cutoff" in the nonbond specification;

!setup nonbond option for GBSW
calc ctonnb = 16.0
calc ctofnb = @ctonnb
calc cutnb  = @ctofnb + 4.0
calc cutim  = @cutnb

NBOND atom switch cdie vdw vswitch -
      ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb cutim @cutim

Once this is done, the rest is the same as gbswmemb1.inp. In other words, once the images are setup, GBSW module automatically consider the influence of the images.

One can setup any kinds of images (in solvent and in membrane) before GBSW setup to consider the influence of those images in GBSW calculations.

gbsw.inp This input illustrates a typical setup for simulations in GBSW solvent without images. The input itself is identical to "gbswmemb1.inp" except the GBSW setup without membrane option;

gbsw sgamma 0.005 nang 50 dgp 1.5

written by Wonpil Im