[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

[Justin Lemkul]

On 11/20/19 4:49 AM, Sun Yeping wrote:
> 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?

You already have what you need - coordinates and topology. A .top is the 
same as .itp except that it defines a system. It should already have all 
the parameters (if needed) and [moleculetype] definition of the ligand. 
Just remove any #include statements to other force field files and any 
[system] or [molecules] directives and it is an .itp that you can use 
directly.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================