[gmx-users] grompp does not find atomtype

Justin Lemkul jalemkul at vt.edu
Wed Jul 2 15:26:14 CEST 2014

On 7/2/14, 9:22 AM, Dawid das wrote:
> 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?

Introduction of custom atom types requires introduction of associated bonded 
parameters.  You can't introduce atoms without defining all the ways that they 
interact.  The proper approach is to add suitable parameters in ffbonded.itp or 
in the .top itself.  If you don't have those parameters, you need to derive them 
or obtain them from some reliable source.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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