Using Leap for ligand

Ligand

% cd ligand_setup % cp ../TAZ.pdb .

Use tleap to create input files for sander

First edit vm1_taz.pdb to remove everything except the TAZ molecule.
Run tleap to make input files for min/md of the ligand alone,create this input file for leap (xleap or tleap):
taz_setup.leapcmd

source leaprc.gaff mods=loadamberparams TAZ.frcmod TAZ = loadmol2 TAZ.mol2 taz=loadpdb vm1_taz.pdb saveamberparm taz taz.prmtop taz.inpcrd quit

Run tleap:

% tleap -f taz_setup.leapcmd

Create a pdb file for viewing:

% ambpdb -p taz.prmtop < taz.inpcrd > taz_leapH.pdb

Run a minimization to clear up bad contacts

Create this file for sander input for simple minimization (same as for protein): min.in

Initial minimisation &cntrl imin=1, maxcyc=500, ncyc=200, cut=16, ntb=0, igb=1, /

Run Sander:

% sander -O -o tazmin.out -i min.in -c taz.inpcrd -p taz.prmtop -r taz_min.inpcrd
% ambpdb -p taz.prmtop < taz_min.inpcrd > taz_min.pdb

Equilibrate:

Create this file, equil.in:

Equilibrate for 40 ps at 400K to shake things up a bit &cntrl imin=0, irest=0, ntx=1, nstlim=20000,ntpr=100, ntc=2,ntf=2,dt=.002, ntwx=100, cut=16, ntb=0, igb=1, ntt=3,temp0=400,tempi=100,gamma_ln=1, /

We will use this pdb file with the minimized ligand structure to constuct the system with the ligand.

Go on to Using Leap to build the complex

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