[gmx-users] atomname2types.n2t explanation
jalemkul at vt.edu
Wed May 24 01:36:07 CEST 2017
On 5/23/17 7:06 PM, Marcelo Depólo wrote:
> Can someone explain what does each column on atomname2types.n2t mean?
> For gromos53a5 it is:
> H H 0.408 1.008 1 O 0.1
> O OA -0.674 15.9994 2 C 0.14 H 0.1
> C CH3 0.000 15.035 1 C 0.15
> C CH0 0.266 12.011 4 C 0.15 C 0.15 C 0.15 O 0.14
> I suppose the first column is the target atom name, the second is the atom
> type, the third is charge and the fourth is mass.
> Is the fifth the number of bonds? And the others?
You've got most of it right, but for the sake of being pedantic so someone can
find it later:
1. Element name, which is used to match the first character in any supplied atom
2. Atom type
3. Atom partial charge
4. Atom mass
5. Number of bonds formed by this atom
6 and onward: the elements and reference bond distances (N entries, where N is
the number found in column 5)
Reference distances behave like any other in GROMACS, if not found within +/-
10% they are not detected.
This information used to be on the wiki but got nuked; it will be added back to
the documentation soon.
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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