[gmx-users] removing dihedral

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 21 22:36:47 CET 2011

Francesco Oteri wrote:
> 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?

The parameters are set to 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


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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