[gmx-users] Unknown bond_atomtype CAY
jalemkul at vt.edu
Wed Sep 21 21:11:13 CEST 2016
On 9/21/16 7:42 AM, Sameer Edirisinghe wrote:
> Dear Dr. Justin,
> Thanks for the explanation. Now i got the point you mentioned here. Then i
> checked the bonds i have mentioned in .rtp file and then i found the
> relevant bonded type. then i checked the ffbonded.itp file and i found that
> bond type is already in there.
> As an example,
> CAY HA1 ; this is one of bond i have in .rtp file. and for that bond,
> relevant bond type (mentioned as below) was already in ffbonded.itp file
> CT HC 1 0.10900 284512.0
> But still following error is occurring while running 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
> How do i refer particular bond types in ffbonded.itp file to my current
> .gro file or any other relevant file ?
grompp won't complain about parameters being missing if they're actually there.
You're probably looking at the wrong line.
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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