[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?

-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
> Fabrício Bracht
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================



More information about the gromacs.org_gmx-users mailing list