[gmx-users] .n2t file format

afsaneh maleki maleki.afsaneh at gmail.com
Fri Jul 19 14:20:56 CEST 2013

 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

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?

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 )?

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

Any help is much appreciated


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