[gmx-users] removing dihedral

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 21 21:21:35 CET 2011

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.


> 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


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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