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atomname2type.n2t
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; Brief: Maps atoms to atom types based on who they are bonded to. Needed for generating topology from .pdb using `gmx x2top`
; Author: Somajit Dey <[email protected]> https://orcid.org/0000-0002-6102-9777
; References :
; 1) For atom_type definitions see "./atomtypes.atp"
; 2) https://manual.gromacs.org/documentation/2019/reference-manual/file-formats.html#n2t
;
; symbol atom_type charge(e) mass(u) n_bonded [symbol_of_bonded bond_length(nm)]...
C pvdf_CH3 -0.62150 12.01100 4 H 0.1085 H 0.1085 H 0.1085 C 0.1534
C pvdf_CH2 -0.52020 12.01100 4 H 0.1085 H 0.1085 C 0.1534 C 0.1534
C pvdf_CF2 0.61200 12.01100 4 F 0.1357 F 0.1357 C 0.1534 C 0.1534
C pvdf_CF3 0.75920 12.01100 4 F 0.1357 F 0.1357 F 0.1357 C 0.1534
H pvdf_H 0.18070 1.00800 1 C 0.1085
F pvdf_F -0.22660 18.99840 1 C 0.1357
;
HJ cnt_H 0.00 1.00800 1 CJ 0.1090 ;Hydrogen
CJ cnt_C 0.00 12.01100 3 CJ 0.1420 HJ 0.1090 HJ 0.1090 ;Periferic C
CJ cnt_C 0.00 12.01100 3 CJ 0.1420 CJ 0.1420 HJ 0.1080 ;Periferic C
CJ cnt_C 0.00 12.01100 1 CJ 0.1420 ;Internal/periodic C
CJ cnt_C 0.00 12.01100 2 CJ 0.1420 CJ 0.1420 ;Internal/periodic C
CJ cnt_C 0.00 12.01100 3 CJ 0.1420 CJ 0.1420 CJ 0.1420 ;Internal/periodic C