Scripts for calculating RESP charges with Gaussian, starting only with .xyz file of your compound.
Generate .mol2, .frcmod and .pdb with calculated RESP charges, for Molecular Dynamic simulations in Amber.
First, use make_esp.sh for run an optimization of your compound (in your desired level of theory) and a single point for ESP calculation, with HF/6-31G* (protocol for RESP charges, read more in https://pubs.acs.org/doi/abs/10.1021/j100142a004).
For neutral molecules in a singlet state, otherwise, change input generation section of make_esp.sh!
files needed: compound.xyz
packages needed: Gaussian; marathon (https://github.com/dudektria/marathon) - for using Gaussian (or change the line where marathon is called, for the method you submit jobs in Gaussian)
usage: ./make_esp.sh xyz(without .xyz) opt_level(scape special characters, for gaussian input) nprocs-opt nprocs-esp
ex: ./make_esp.sh compound MP2/6-311G\* 8 2
or
nohup ./make_esp.sh compound MP2/6-311G\* 8 2 & (still running, even if you exit terminal, in background)
Press enter each gaussian run finishes.
Before, use make_resp.sh for generating compound.mol2, compound.frcmod and compound.pdb with calculated RESP charges.
files needed: compound_esp.out (output from ESP calculation)
packages needed: antechamber; parmchk
usage: ./make_resp.sh esp_output(without _esp.out) residue_name
ex: ./make_resp.sh compound RES