[gmx-users] grompp does not find atomtype
addiw7 at googlemail.com
Wed Jul 2 15:31:07 CEST 2014
Excuse me but I don't think we understand each other. If there are three
atoms for instance and two of them are bonded and the third is not then how
can I obtain or derive parameters for them? That is what I do not
2014-07-02 15:29 GMT+02:00 Dawid das <addiw7 at googlemail.com>:
> 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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