[gmx-users] problems running grompp with protein-ligand complex

Ragnarok sdf fabracht1 at gmail.com
Wed Nov 26 23:27:10 CET 2008

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:
Fatal error:
Found a second defaults directive, file "ligand.itp", line 5
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.
I would like some advice on the matter if possible.
Thank you in advance
Fabrício Bracht
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