#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 TYPE), # where Atom_Name1 belongs to the residue and Atom_Name2 belongs to the cap. When TYPE is # 1, ATOM_NAME1, the HEAD_ATOM, is connected to the immediate proceeding residue, such as # N of an amino acid; when TYPE is -1, ATOM_NAME1, the TAIL_ATOM, is connected to the # immediate succeeding residue, such as C of an amino acid; when TYPE is 0, it is just # used to trunctat unwanted atoms (such as extra side chain atoms). SEP_BOND may show up # several times or not show up at all. SEP_BOND N1 C2 1 SEP_BOND C5 N2 -1 #PSEUDO_HEAD_ATOM: Psedu_head_atom is used to model N-terminal amino acid residues, such as NALA or 5' # -nucleic acid residue, such as DC5. Input in a format of (Atom_Name), may show up only # once (amino-acid-like and nucleic-acid-like terminal residues) or not show up at all # for organic molecules. This option is suppressed by a SEP_BOND with TYPE of 1. PSEUDO_HEAD_ATOM N1 #PSEUDO_TAIL_ATOM: Psedu_tail_atom is used to model C-terminal amino acid residues, such as CALA or 3' # -nucleic acid residue, such as DC3. Input in a format (Atom_Name), may show up only # once (amino-acid-like and nucleic-acid-like terminal residues) or not show up at all # for organic molecules. This option is suppressed by a SEP_BOND with TYPE of -1. PSEUDO_TAIL_ATOM C5 # Main chain atoms are those starting from HEAD_ATOM or PSEUDO_HEAD_ATOM and ending at # TAIL_ATOM or PSEUDO_TAIL_ATOM for the amino-acid-like or nucleic-acid-like residues. # For organic molecules, main chain atoms are those forming the longest chain. Main # chain atoms are identified automatically (not need to specify). #NET_CHARGE: Net charge of the residue, such as 0 of ALA and -1 of ASP and 1 of LYS # this option is ignored when the number of SEP_BOND lines is zero NET_CHARGE 0 #ATOM_CHARGE: Predefined atom charge, input in a format of (Atom_Name Partial_Charge) # can show up multiple times. 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