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

[Mark Abraham]

Hi,

Topologies are specific to force fields. You still need to go and
understand how they should be used. And probably to choose your force field
and topology generation method based on what science you want to achieve.
:-)

Mark

On Fri, 5 May 2017 20:49 Syed Azeem <syedazeemullah186 at gmail.com> wrote:

> 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
> --
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