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

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 26 23:40:40 CET 2008

Can you post the contents of your ligand.itp?


Ragnarok sdf wrote:
> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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