TINKER script to minimize .pdb files

tinkermin

#!/bin/bash

# Input pdbfile, force field key, optimization convergence
PDB=$1
FF=$2
CONV=$3

TINKERBIN=/home/andersx/programs/tinker/bin


# Convert PDB to tinker XYZ using the keyfile
${TINKERBIN}/pdbxyz.x ${PDB} -k ${FF}

# Minimize using the tinker XYZ, keyfile and convergence argument
${TINKERBIN}/minimize.x ${PDB%.*}.xyz -k ${FF} ${CONV}

# Convert resulting tinker XYZ to pdb
echo ${TINKERBIN}/xyzpdb.x ${PDB%.*}.xyz -k ${FF} to convert to pdb