[gmx-users] .n2t file format

[Justin Lemkul]

On 7/19/13 8:20 AM, afsaneh maleki wrote:
>   Dear gmx users
>
>
> I scrap lines from some files in oplsaa.ff folder as the following
>
> ffnonbonded file:
>
> [ atomtypes ]
>
> opls_157   CT    6     12.01100     0.145       A    3.50000e-01
> 2.76144e-01
>
> atomtypes.atp file:
>
> opls_157   12.01100  ; all-atom C: CH3 & CH2, alcohols
>
> also, I looked at /gromacs /Documentation/file format/.n2t that written:
>
> To translate atom names into atom types, the x2top program uses library
> files called .n2t files as input. These files contain information about
> atom types, charges, and connectivity to neighbors. The format of such a
> file is exemplified by:
>
>
>
> *C* opls_157  -0.18  12.011  4  H  0.108  H 0.108  H 0.108  C 0.150
>
>
>
> The above line interprets an atom named C to be the carbon atom in CH3,
> CH2, or alcohols (atom type opls_157).
>
>
>
> My question is that carbon atomname with opls_157 atomtype is *C* or CT?
>

The type is opls_157 for the purposes of ffnonbonded.itp, which is translated to 
the CT in ffbonded.itp.

> In other word the first column in .n2t is atomneme (CT as mentioned in
> ffnonbonded file ) or element name (C as mentioned in file format.n2t )?
>

In Gromacs nomenclature, atom names are whatever is read from the input 
coordinate file (no differentiation between atom name and element name) and atom 
types are force field-specific.

> Also, are 6, 8 10 columns atomname or element name?
>

Both, given Gromacs' interpretation of atom names.  g_x2top will look for 
matches based on whatever element it finds, so in the case of column 6, any of 
these will match: H, HA, H1, H2, etc.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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