[gmx-users] atomname2types.n2t explanation

[Justin Lemkul]

On 5/23/17 7:06 PM, Marcelo Depólo wrote:
> Hi
>
>
> 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 
name
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

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

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
http://mackerell.umaryland.edu/~jalemkul

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