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.<br>
I've tested this procedure once with a different system using ffgmx forcefields and everything went all right. However, now that i am using ffamber99 forcefield everything seems to be working against me. It took me quite some time to figure out how to generate topology files for ligands with this forcefield. So I would really aprecciate some help on the matter.<br>
Thank you in advance<br>Fabrício Bracht<br>