[gmx-users] How to prepare prm and itp files of ligands from gro and top files prepared with Gauss, ambertool and acpye for gromacs simulations

[Sun Yeping]

Dear everyone,

In order to perform gromacs simulations with ligand-protein complex, I have
to prepare the force field files for the ligand.
I first use Gauss to generate a Lig.gesp file which describe the
electrostatic potential. Then I use antechamber  from ambertool to fit the
gesp charges and generate a lig.mol2 file.

      antechamber -i Lig.gesp -fi gesp -o Lig.mol2 -fo mol2 -pf y -c resp

After that, I use parmchk2 to generate the frcmod file

      parmchk2 -i Lig.mol2 -f mol2 -o Lig.frcmod

Then the Lig.inpcrd coordinate file is prepared by tleap program from
ambertool, following which I use the acpye the generate the top and gro
files.

     acpype -p Lig.prmtop -x Lig.inpcrd -d

Now I have Lig.gro and Lig.top files in hand. However, to perform gromacs
simulation, I need the .prm and .itp files. Could you tell me how to get
these files?

Best regards.