1. Preparation of ligand with RESP charges using Gaussian and antechamber
Ayesha Fatima

2. Method Get the pdb or mol2 file of ligand with hydrogen atoms included
2. Execute command in Ubuntu terminal:
antechamber -i x.pdb -fi pdb -o x.dat -fo gert -gv 1 -ge x.gesp
Output file is “.dat”
Rename .dat file to .gjf for use in gaussian
Execute Gaussian for calculation of RESP charges by entering command
g09 < x.gjf > x.out&
Output is ‘.gesp’ file
Use antechamber to get a ‘prepi’ file
antechamber -i x.gesp -fi gesp -o x.prepi -fo -prepi -c resp -eq1 -nc 0 -s o –at amber -rn x
Use the following command to get the frcmod file
parmchk -i x.prepi -f prepi -o x.frcmod

3. Output frcmod file remark goes here MASS BOND ANGLE DIHE IMPROPER
c3-o -c -os General improper torsional angle (2 general atom types)
c -c3-n -c General improper torsional angle (1 general atom type)
n -o -c -os General improper torsional angle (2 general atom types)
NONBON