[gmx-users] grompp does not find atomtype

Dawid das addiw7 at googlemail.com
Wed Jul 2 15:29:10 CEST 2014

Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for

2014-07-02 15:22 GMT+02:00 Dawid das <addiw7 at googlemail.com>:

> 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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