[gmx-users] removing dihedral

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 21 21:00:29 CET 2011

francesco oteri wrote:
> Dear gromacs users,
> I am trying to build the topology for a protein-ligands system. When I 
> run grompp I obtain 96 of the following errors:
> ERROR 1 [file topol_Protein_chain_S.itp, line 38658]:
>   No default Proper Dih. types
> The errors correctly says that dihedral parameters are missing for my 
> ligands. 
> My question is, there is a method to avoid considering such a dihedrals, 
> avoiding topology editing?
> In other words, I don't wanna edit the .top file removing by-hand the 
> lines generating the error. 

If you're missing parameters, you need to assign them.  Whether or not that 
requires deriving new dihedral types depends on the complexity of the molecule.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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