#sample residuegen input file

#INPUT_FILE:	structure file in ac format, generated from a Gaussian output with 'antechamber'
#             	(Cmd: antechamber -fi gout -fo ac -i input.gout -o output.ac)
INPUT_FILE    	ala.ac

#CONF_NUM: 	Number of conformations applied
CONF_NUM    	2

#ESP_FILE:   	esp file generated from gaussian output with 'espgen'
#             	(cmd: espgen -i input.gout -o output.esp)
# 	      	if multiple conformations applied, catenate all the CONF_NUM esp files into ESP_FILE
#             	(cmd: cat output1.esp output2.esp output3.esp ... > output.esp)
ESP_FILE    	ala.esp

#SEP_BOND: 	bonds that separate residue and caps, input in a format of (Atom_Name1 Atom_Name2), 
#		where Atom_Name1 belongs to residue and Atom_Name2 belongs to a cap. 
#		must show up twice times for amino-acid-like or nucleci-acid-like residues or none of
#		normal organic molecules
SEP_BOND    	N1 C2
SEP_BOND 	C5 N2 

#NET_CHARGE: 	net charge of the residue, such as 0 of ALA and -1 of ASP and 1 of LYS
#		This option is ignored for a normal organic molecule, for which the net charge of
#               the whole molecule is read in from the INPUT_FILE)
NET_CHARGE   	0

#ATOM_CHARGE: 	predefined atom charge, input in a format of "Atom_Name Partial_Charge",
#              	can show up multiple times or not show up at all. 
ATOM_CHARGE   	N1 -0.4175  
ATOM_CHARGE   	H4 0.2719
ATOM_CHARGE   	C5 0.5973 
ATOM_CHARGE   	O2 -0.5679  

#PREP_FILE: 	prep file name 
PREP_FILE:  	ala.prep

#RESIDUE_FILE_NAME: 	residue file name in PREP_FILE
RESIDUE_FILE_NAME:  	ala.res

#RESIDUE_SYMBOL: 	residue symbol in PREP_FILE
RESIDUE_SYMBOL:  	ALA