I am attempting to prepare an array of files to be run on AMBER. In this preparation, LEaP is used to solvate the receptor and ligand. I have attempted to script the preparation as I have a lot of simulations that I plan to run, however I am unsure of the syntax that needs to be used to inject the input for LEaP in the script file.
How would I prepare a simple script that puts in my initial parameter preparation commands (antechamber, parmchk etc) then launches LEaP and runs commands in that tool?
My current script is as follows:
antechamber -i ligand.mol2 -fi mol2 -o ante.prep -fo prepi -c bcc
parmchk -i ante.prep -f prepi -o lig.frcmod
set default PBRadii mbondi2
source leaprc.water.tip3p
source leaprc.gaff2
loadamberparams lig.frcmod
loadamberprep ante.prep
LIG = loadpdb NEWPDB.PDB
REC = loadpdb rec.pdb
MD = combine {REC LIG}
savepdb MD input.pdb
saveamberparm MD input.prmtop input.inpcrd
charge MD
solvatebox MD TIP3PBOX 11
savepdb MD solvated.pdb
saveamberparm MD solvated.prmtop solvated.inpcrd
quit
The LEaP console launches, but then I can't figure out how to get the script to read the commands I want to use for LEaP (the indented commands) into the LEaP console.
Can you share an example of what a couple of sets of parameters/commands would look like?
Where are you sourcing the information for each parameter etc that goes in to the script?