Question: Scripting AMBER Preparation files
gravatar for protein_fashion
15 months ago by
protein_fashion0 wrote:

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

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.

ADD COMMENTlink modified 15 months ago • written 15 months ago by protein_fashion0

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?

ADD REPLYlink written 15 months ago by Joe18k
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