1#!/bin/bash
2
3module load ambertools23
4
5ligand=$1
6charge_method="bcc"
7verbose=2
8net_charge=0
9resname="lig"
10intermediate_files="yes" # delete
11
12if [ -z "${ligand}" ]; then
13 echo "NOT FOUND: Requires the ligand PDB file!!!"
14 exit 1
15fi
16
17if grep -q ".pdb" ${ligand}; then
18 filename=$(awk -F "." '{print $1}')
19 fileformat=$(awk -F "." '{print $1}')
20else
21 echo "Assuming PDB file"
22 filename=${ligand}
23 fileformat="pdb"
24 name=$(echo ${ligand} | sed 's/.pdb//')
25fi
26
27antechamber \
28 -i ${filename}.${fileformat} \
29 -fi ${fileformat} \
30 -o ${filename}.mol2 \
31 -fo mol2 \
32 -c ${charge_method} \
33 -s ${verbose} \
34 -nc ${net_charge} \
35 -rn ${resfilename} \
36 -pf ${intermediate_files}
37
38if [ -f parmchk2.sh ] && [ ! -f "${filename}.frcmod" ]; then
39 parmchk2 -i ${filename}.mol2 -f mol2 -o ${NAME}.frcmod
40elif [ ! -f "parmchk2.sh" ] && [ ! -f "${filename}.frcmod" ]; then
41 echo "NOT FOUND: parmchk2.sh - required for frcmod !!!"
42else
43 echo "Found frcmod file.. Skipping parmchk2."
44fi
