[gmx-users] removing dihedral

Francesco Oteri francesco.oteri at gmail.com
Mon Nov 21 21:32:12 CET 2011

ffbonded.itp is right, grompp misses only a particular dihedral. 
Everithing is fine for bond, angle and some dihedrals.
What exactly means "zeroing out all terms for the unknown dihedrals"? It 
means that are not present in tpr or that parameters (i.e reference 
angle, multiplicity,...)
are zero?

Il 21/11/2011 21:21, Justin A. Lemkul ha scritto:
> Francesco Oteri wrote:
>> 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?
> Well, using "grompp -zero" will bypass the error by zeroing out all 
> terms for the unknown dihedrals.  If there are 96 of them, that means 
> you will have completely incorrect bonded interactions.
> If you have parameters that should work for this particular molecule, 
> they are not being found in ffbonded.itp.  That's the problem.  So you 
> can resolve the problem by adding bonded parameters to that file or 
> defining them locally in your .top with a suitably placed [dihedrals] 
> (or whatever else) directive.
> -Justin
>> 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

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