Tutorial on running Molecular Dynamics for GIST grid generation
Tutorial written by Trent Balius (Jan. 9, 2017).
This is foremost for training Shoichet lab members. But we hope that the community finds this useful.
To use this tutorial you will need the following:
- AMBER12 or higher.
- GPUs to run AMBER on. In our case we uses an SGE queuing system to manage these jobs.
- It is helpful if you have DOCK3.7 the latest version.
Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodynamic properties of water on GIST lattice.
Here, we will use these grids for DOCKing (although, there are many other uses).
Set up environment
you can add the following to your environment file (.cshrc) for just issue them on the command line.
source python with bio_python package.
setenv DOCKBASE "/nfs/home/tbalius/zzz.github/DOCK"
Put msms in your path
set path = ( /nfs/home/tbalius/zzz.programs/msms $path )
Set up directories
mkdir ambergisttutorial cd ambergisttutorial
Prepare for AMBER
- download 4NVE form the PDB brake it into receptor and ligand pieces.
- download pdb 4NVA form the PDB align it to 4NVE and out put waters that are close to the ligand.
- here is one way to do it:
break up the protein from the ligand. run be_blasti.py
$DOCKBASE/proteins/pdb_breaker/be_blasti.py --pdbcode 4NVE nocarbohydrate original_numbers | tee -a pdbinfo_using_biopython.log
$DOCKBASE/proteins/pdb_breaker/be_blasti.py --pdbcode 4NVA nocarbohydrate original_numbers | tee -a pdbinfo_using_biopython.log
cd 4NVE sed -e "s/HETATM/ATOM /g" lig.pdb > xtal-lig.pdb cd ../
cd 4NVA grep HOH $mountdir/workingdir/4NVA/4NVA_A.pdb > $workdir/water.pdb cd ../
Next align the two receptors (4NVE to 4NVA) and find those waters close to the ligand.
create file named "chimera.com" and write the following into the file:
# Gist template #0 open ../4NVA/rec.pdb # 4NVE rec open ../4NVE/rec.pdb # 4NVE lig open ../4NVE/lig.pdb # 4NVA waters open ../4NVA/water.pdb mmaker #0 #1 matrixcopy #1 #2 sel #3:HOH & #2 z<8 del #3 & ~sel write format pdb 0 template.pdb write format pdb 1 aligned.rec.pdb write format pdb 2 aligned.lig.pdb write format pdb 3 close.waters.pdb
/nfs/soft/chimera/current/bin/chimera --nogui chimera.com > & chimera.com.out