On 9/18/16 10:14 PM, Sameer Edirisinghe wrote:
Dear Dr. Justin,

If the bond types have not added, following errors occuring with grompp,

1) ERROR 1 [file topol.top, line 108]:
  No default Bond types

2) ERROR 2 [file topol.top, line 168]:
  No default Angle types

3) ERROR 3 [file topol.top, line 426]:
  No default Ryckaert-Bell. types

Atom types are seems to be correct as i derived them from atomtype.atp
file.

If the interaction don't cover by the force field, how can I define them in
ffbonded.itp file ?


See the manual. Use atom types, not names. If you're adding parameters, be sure they've been derived properly. If you're still using anything from that PRODRG topology and trying to force it into OPLS-AA, don't.

-Justin

--
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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