[gmx-users] Grommp Fatal Error (Syed Azeem)

[Syed Azeem]

Hey Mark,

Thanks for the reply. I even tried other force fields, which yielded
the same errors. For Gromos 53a6 ff, "No default Ryckaert-Bell types"
was included in the error.

> Hi,
>
> grompp will always need angle type definitions for the angles in the .itp
> file - they have to either be in the force field already, or added to it.
> If they are not present in amber99sb-ildn, then you need to understand how
> the topologies were generated and how they are intended to be used in order
> to make an appropriate choice.
>
> Mark
>
> On Fri, May 5, 2017 at 12:48 PM Syed Azeem <syedazeemullah186 at gmail.com>
> wrote:
>
>> Hi all,
>>
>> I'm trying to simulate a Protein-Peptide docked complex.
>> I used Amber99sb-ildn ff with TIP3P. Since mine is a docked complex,
>> two separate topology and position restraint files were created as
>> chains A & B, automatically.
>>
>> When I tried to generate the .tpr file for adding ions to the system,
>> I ended up with 3 errors in the topology file of chain A. The error
>> corresponded to [angles] and [dihedrals] of chain A.
>>
>> Error message:
>>
>> ERROR 1 [file topol_Protein_chain_A.itp, line 46901]:
>>   No default Angle types
>>
>>
>> ERROR 2 [file topol_Protein_chain_A.itp, line 65796]:
>>   No default Proper Dih. types
>>
>>
>> ERROR 3 [file topol_Protein_chain_A.itp, line 65798]:
>>   No default Proper Dih. types
>>
>> How to overcome this error?
>>
>> Thanks in advance
>>
>> Azeem