Using Leap

Protein

% cd prot_setup

Use tleap to create input files for sander

Run tleap to make input files for min/md of the protein alone,create this input file for leap (xleap or tleap): prot_setup.leapcmd

source leaprc.ff03 vprot=loadpdb vm1_prot.pdb bond vprot.77.SG vprot.123.SG saveamberparm vprot vm1_prot.prmtop vm1_prot.inpcrd quit

Run tleap:

% tleap -f prot_setup.leapcmd

Create a pdb file for viewing:

% ambpdb -p vm1_prot.prmtop < vm1_prot.inpcrd > vm1_prot_leapH.pdb

Run a minimization to clear up bad contacts

Create this file for sander input for simple minimization: min.in

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

Run Sander:

% sander -O -o protmin.out -i min.in -c vm1_prot.inpcrd -p vm1_prot.prmtop
% mv restrt vm1_prot_min.inpcrd
% ambpdb -p vm1_prot.prmtop < vm1_prot_min.inpcrd > vm1_prot_min.pdb

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

Go on to Using Leap for ligand
Back to introduction