[gmx-users] ligand protein complex with ffamber99

[Mark Abraham]

Ragnarok sdf wrote:
> I am trying to setup a simulation with a ligand and a protein using 
> ffamber99 forcefield. I have already generated the ligand's topology 
> file using acpypi and everything seems to be all right in the files 
> generated. However, while following the steps in the drug enzyme 
> tutorial provided in the gromacs' web site, after i add the ligand to my 
> protein's .gro file and edit the lines in my topology file to include 
> the ligand's topology, when i type the command editconf, my ligand 
> dissapears from my .gro file. The .gro generated from my original 
> ligand-protein complex.gro does not include my ligand coordinates 
> whatsoever.

I'm guessing you've added your ligand to the end of the file, but not 
adjusted the total number of atoms at the top of the file.

Mark