[gmx-users] grompp does not find atomtype

Dawid das addiw7 at googlemail.com
Wed Jul 2 15:22:20 CEST 2014

2014-07-02 13:50 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

> The problems almost certainly stem from the manipulations you've made to
> the angles and dihedrals.  I don't understand why you've commented some of
> them out.  For instance, the first angle that you've removed is atoms
> 977-978-992, which clearly should have an angle interaction because 977-978
> and 978-992 are bonded.  Simply removing "inconvenient" interactions (i.e.
> lacking parameters or whatever) leads to a total meltdown of the model.

Okey, but what should I do if there are missing parameters for combination
of atoms which are not bonded?
For instance: 973-977-978-992 atoms are not bonded but still in *top there
is an "torsion interaction" for these atoms? What does it mean? It seems
like some of the atom types are confused? Is it possible that I defined
them in ambigous way?

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