[gmx-users] Atomtype P,SI not found from grompp
jalemkul at vt.edu
Thu Jan 15 19:38:11 CET 2015
On 1/15/15 1:31 PM, Jennifer Vo wrote:
> Dear Justin,
> Thanks a lot, now I got it. I thought P and SI is the two separated atoms
> so I searched for them two times. Now the
> grep "P,SI" *.*
> nap_allatom.itp: 3 P,SI 1 NAP P2B 1 2.247 30.9738
> nap_allatom.itp: 21 P,SI 1 NAP PA 4 2.315 30.9738
> nap_allatom.itp: 26 P,SI 1 NAP PN 5 2.259 30.9738
> should I change "P,SI" to P only?
If the atom name is an indicator of what the atom is, then presumably yes. But
I would be wary of any topology in general that used nonsense atom types in the
parameters it produces, unless there is some additional (external) set of
parameters upon which this molecule relies, e.g. something that defines new
parameters and interactions for something called "P,SI."
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
More information about the gromacs.org_gmx-users