[gmx-users] grompp does not find atomtype

Justin Lemkul jalemkul at vt.edu
Wed Jul 2 15:34:42 CEST 2014

On 7/2/14, 9:29 AM, Dawid das wrote:
> 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
> them.

Inspection of a coordinate file tells you nothing about the bonded structure. 
Look at the topology, line 4712:

    978   992     1    0.1350 127612.0

That says atoms 978 and 992 are bonded, and you have defined the parameters for 
that bond manually.


> 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?


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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