[gmx-users] removing dihedral

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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