[gmx-users] removing dihedral

[Francesco Oteri]

I am using parameters already developed for CHARMM. So I guess the 
parameters are right and I am sure there is no error in the trasformation
from CHARMM to GROMACS format. May the option "-zero" in grompp solve my 
problem?


Il 21/11/2011 21:00, Justin A. Lemkul ha scritto:
>
>
> 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
>