Computational Drug Discovery and Design

water molecules, local ions, solvent, and salt concentration of

150 mM NaCl should resemble Fig.9.

Step 12. Obtain system box information.

• NAMD requires the dimensions of the initial system box as
  input. Additionally, the user can specify a box center as the origin
  for molecule wrapping. Obtain the box dimensions and center
  of the protein–drug complex by entering the following com-
  mands:

set all [atomselect top "all"] ; # Select system and measure box dimensions
set dimens [vecsub [lindex [measure minmax $all] 1] [lindex [measure minmax $all] 0]]
set complex [atomselect top "protein or resname TYL"] ; # Select complex and measure center
set center [measure center $complex]

• Note that the x-, y-, and z-values of the box dimensions and
  wrapping center are entered as NAMD inputs in the following
  section.

Step 13. Minimize potential energy of the system.

• Open a terminal and navigate to your working directory. Make
  sure that the location of the NAMD executable is contained
  within your $PATH variable.


• Save the NAMD configuration script given below to your work-
  ing directory as min.conf.

Fig. 9The final model of the aryl acylamidase–acetaminophen complex within a

native solvent environment

Molecular Dynamics Simulations of Protein-Drug Complexes 261