[gmx-users] Atomtype P,SI not found from grompp

Justin Lemkul 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" *.*
> returned
> 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


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