[gmx-users] Charges and Antechamber

[ABEL Stephane]

HI 

It is quite easy to derive RESP charges and use them with GROMACS. You could follow the steps

1) Build a pdb file of your molecule/modified residue 
2)  Use the web server pyRED (http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive the RESP charges. The webserver will also give you all the necessary parameters of the ff (mol2 file, atom types, (non)bonded parameters)
3) Use these parameters to construct a rtp file for GROMACS for a given force field
4) and finally use pdb2gmx with the pdb file to obtain the itp file.  

That's all 

Good luck