optimization_script.sh

#!/bin/bash

#######################################################################################
#     –––––– This is a script for optimize geometry of library ligands ––––––	      #
# AUTOR: ROPÓN-PALACIOS G., BSc, MSc(c),		                              #
# 		 Bioinformatics & Theoretical Biophysics – Molecular Genetics Lab,    #
#		 Departament of Biology & Physics, Faculty of Sciences,               #
#		 Universidad Nacional de San Antonio Abad del Cusco	              # 
#                Av. La Cultura 733, Wanchaq, Cusco, Peru.			      #               
#		 E-mail: biodano.geo@gmail.com					      #
#######################################################################################

# Run script using obminimize module of Openbabel:
for i in out_*.pdb; do 
	b=`basename $i .pdb`
	echo Processing ligando $b
	mkdir -p $b
	obminimize -ff MMFF94 -n 10000 -sd -c 1e-9 $i; 
done 

# -ff is a force field option
# -n numbres de steps 
# -sd algortirm of steps descendent
# -c energy max 

# REMEMBER:
# If you are usign this script please, cited link of github
# For more information o problems please send me a e-mail.