3.2 Preparation
of MD Input Files
- Prepare the whole system for the MD simulations in tleap by
creating a solvated periodic box and adding charge neutralizing
ions. The script may look like this:
source leaprc.ff03
set default PBradii mbondi2
mol=loadpdb prot.pdb
check mol
charge mol #(determine the net charge of the system)
bond mol.10.SG mol.20.SG #(example of a bridge between Cys10 and Cys20)
solvatebox mol TIP3PBOX 10 #(create a cubic periodic box with 10A ̊ between the
protein and the box edge)
addions mol Na+ 0 #(neutralize charges; use either Na+ or Cl-)
saveamberparm mol sys.prmtop sys.inpcrd #(create topology files)
savepdb mol sys.pdb #(optionally save the new PDB file)
quit
- The MD protocol we follow executes first of all a rapid minimi-
zation of the solvent by the steepest descent algorithm. The
solute is restrained by a harmonic potential with the force
constant equal to 100 kcal/mol/A ̊^2. The typical values of
different parameters are given in the script below:
Initial energy minimization—step 1 (solvent only)
&cntrl
imin=1, ncyc=500, maxcyc=500,
ntb=1, cut=12, ntr=1
/
Hold the solute fixed
100.0
RES 1 291
END
ENDIn the above, 291 is the number of residues of the receptor
including any cofactor or ligand residues, and should be adjusted as
needed. As for the choice of the cutoff, the general rule is that the
box size should be at least twice the cutoff plus a margin of 1–2 A ̊.
Since the distance between a protein and the box edge is 10 A ̊ on
each side, the box size is twice this value plus the diameter of the
protein, in total ca. 40 A ̊ in this example. Since the cutoff was
defined as 12 A ̊, the above rule is satisfied. For the description of
other parameters, see the relevant manuals on the Web pagehttp://
ambermd.org/doc12.
The second stage is a more thorough minimization, where the
initial 500 iterations of the steepest descent are followed by 1500
iterations (maxcyc-ncyc) of the conjugate gradient algorithm. This152 Gre ́gory Menchon et al.