[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 jalemkul at vt.edu
Thu Nov 21 02:20:32 CET 2019



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
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Virginia Tech Department of Biochemistry
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