Can you post the contents of your ligand.itp?
-Justin
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
FabrÃcio 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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