Hi Wiktor Łachmański

You can use ACPYPE to generate topology file along with coordinate (gro) and include topology file (itp).

Hi,

This could be an example of topol.op

; Include forcefield parameters

#include "charmm27.ff/forcefield.itp"

#include "ret_all_trans.itp"

; Include water topology

#include "charmm27.ff/spc.itp"

;

; Include topology for ions

#include "charmm27.ff/ions.itp"

;

#ifdef POSRES_WATER

; Posiion resraint for each water oxygen

[position_restraints ]

;i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

;

[ system ]

; Name

neutral en agua

[ molecules ]

; Compound #mols

ret_all_trans 1

SOL 1134

You can solve this issue by following the normal steps to simulate a common protein but considerng your ligand instead protein to obtain your topol.top file, then add the ligand force field (DRGGMX.itp), which your can easily obtain from the PRODRG server, into the topol.top (line ; Include forcefield parameters).

Good simulation