I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that:<br>
Fatal error:<br>Found a second defaults directive, file "ligand.itp", line 5<br>I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line.<br>
I would like some advice on the matter if possible.<br>Thank you in advance<br>Fabrício Bracht<br>