On 7/2/14, 9:22 AM, Dawid das wrote:
2014-07-02 13:50 GMT+02:00 Justin Lemkul <jalem...@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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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