[gmx-users] .top files
Pedro Alexandre Lapido Loureiro
paloureiro at biof.ufrj.br
Thu Oct 31 19:36:48 CET 2002
Thank you Erik and Marcos for your answers, but I am still a bit confused.
If you don't mind, I will send you a short version of my .top file:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 yes 1.0 0.5
#define _FF_GROMACS
#define _FF_GROMACS1
[ atomtypes ]
#ifdef HEAVY_H
OW 9.95140 0.000 A 0.26171E-02 0.26331E-05
HW 4.03200 0.000 A 0.00000E+00 0.00000E+00
#else
OW 15.99940 0.000 A 0.26171E-02 0.26331E-05
HW 1.00800 0.000 A 0.00000E+00 0.00000E+00
#endif
LNL 14.00670 0.000 A 0.33514E-02 0.39494E-05
LO2 15.99940 0.000 A 0.23621E-02 0.15887E-05
LOS 15.99940 0.000 A 0.20733E-02 0.15114E-05
LP 30.97380 0.000 A 0.91516E-02 0.25045E-04
LC 12.01100 0.000 A 0.48722E-02 0.13549E-04
LCH1 13.01900 0.000 A 0.40226E-02 0.12112E-04
LCH2 14.02700 0.000 A 0.58616E-02 0.22604E-04
LCH3 15.03500 0.000 A 0.87924E-02 0.33906E-04
LC3N 15.03500 0.000 A 0.93477E-02 0.36047E-04
LC2 14.02700 0.000 A 0.70067E-02 0.24845E-04
LC2O 14.02700 0.000 A 0.59496E-02 0.17914E-04
; C 12.01100 0.000 A 0.23402E-02 0.33740E-05
C 12.01100 0.000 A 0.197782E-02 0.305534E-05 ;Scharf
; H 1.00800 0.000 A 0.00000E+00 0.00000E+00
H 1.00800 0.000 A 0.144043E-03 0.623001E-07 ;Scharf
; CL 35.45300 0.000 A 0.13804E-01 0.10691E-03
CL 35.45300 0.00 A 0.67868E-02 0.12476E-04 ;Scharf
; F 18.99840 0.000 A 0.78301E-02 0.25209E-04
F 18.99840 0.00 A 0.59277E-03 0.28565E-06 ;Scharf
BR 79.90400 0.000 A 1.26285E-02 0.324013Ee-04 ; Scharf
; BR 79.90400 0.000 A 0.11792E-02 0.65480Ee-04 ;Loureiro
MW 0 0.000 A 0.0 0.0
[ bondtypes ]
; i j func b0 kb
HW OW 1 0.10000 418400.
LNL LC3N 1 0.147 376560.
LNL LC2 1 0.147 376560.
LC2 LC2O 1 0.153 334720.
LOS LC2O 1 0.143 251040.
LOS LP 1 0.161 251040.
LO2 LP 1 0.148 376560.
LO2 LC 1 0.123 502080.
LCH1 LC2O 1 0.153 334720.
LOS LCH1 1 0.143 251040.
LOS LC 1 0.136 251040.
LC LCH2 1 0.153 334720.
LCH2 LCH3 1 0.153 334720.
LCH2 LCH2 1 0.153 334720.
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 109.500 502.080
LC3N LNL LC3N 1 109.5 460.24
LC3N LNL LC2 1 109.5 460.24
LNL LC2 LC2O 1 109.5 460.24
LC2 LC2O LOS 1 109.5 460.24
LC2O LOS LP 1 120.0 397.48
LOS LP LO2 1 109.6 397.48
LOS LP LOS 1 103.0 397.48
LO2 LP LO2 1 120.0 585.76
LOS LC2O LCH1 1 111.0 460.24
LC2O LCH1 LOS 1 109.5 460.24
LC2O LCH1 LC2O 1 109.5 460.24
LCH1 LOS LC 1 120.0 418.40
LC2O LOS LC 1 120.0 418.40
LOS LC LO2 1 124.0 502.08
LOS LC LCH2 1 115.0 502.08
LO2 LC LCH2 1 121.0 502.08
LC LCH2 LCH2 1 111.0 460.24
LCH2 LCH2 LCH2 1 111.0 460.24
LCH2 LCH2 LCH3 1 111.0 460.24
[ dihedraltypes ]
; j k func phi0 cp mult
LNL LC2 1 0.0 3.7656 3
LC2 LC2O 1 0.0 5.8576 3
LOS LC2O 1 0.0 3.7656 3
LOS LP 1 0.0 1.046 3
LCH1 LC2O 1 0.0 2.092 2
LOS LCH1 1 0.0 3.7656 3
LOS LC 1 180.0 16.736 2
LC LCH2 1 0.0 0.4184 6
LCH2 LCH2 1 0.0 5.8576 3
[ dihedraltypes ]
LCH2 LCH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
[moleculetype]
;Name nrexcl
DPPC 3
HAL 3
[atoms]
; nr type resnr residu atom cgnr charge ; Chiu charges!
1 LC3N 1 DPPC CN1 1 0.40
2 LC3N 1 DPPC CN2 1 0.40
3 LC3N 1 DPPC CN3 1 0.40
4 LNL 1 DPPC NTM 1 -0.50
5 LC2 1 DPPC CA 2 0.30
etc.
46 LCH2 1 DPPC C2L 32 0.0
47 LCH2 1 DPPC C2M 33 0.0
48 LCH2 1 DPPC C2N 34 0.0
49 LCH2 1 DPPC C2O 35 0.0
50 LCH3 1 DPPC C2P 36 0.0
51 F 2 HAL F1 37 -0.6167 18.99840
52 F 2 HAL F2 38 -0.6196 18.99840
53 F 2 HAL F3 39 -0.6231 18.99840
54 C 2 HAL C4 40 1.7762 12.01100
55 C 2 HAL C5 41 0.0760 12.01100
56 H 2 HAL H6 42 0.1349 1.00800
57 BR 2 HAL BR7 43 -0.0100 79.90400
58 CL 2 HAL CL8 44 -0.1349 35.45300
[bonds]
; ai aj funct
1 4 1
2 4 1
3 4 1
etc
46 47 1
47 48 1
48 49 1
49 50 1
51 54 1 0.13600 418400. 0.13600 418400.
52 54 1 0.13600 418400. 0.13600 418400.
53 54 1 0.13600 418400. 0.13600 418400.
54 55 1 0.15300 418400 0.15300 418400
55 56 1 0.10900 245843. 0.10900 245843.
55 57 1 0.19570 418400. 0.19570 418400. ;modificado
55 58 1 0.17790 418400. 0.17790 418400.
[pairs]
etc
[angles]
etc
[dihedrals]
etc
; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif
[ system ]
; Name
DPPC/HAL in Water
[ molecules ]
; Compound #mols
DPPC 64
SOL 4597
DPPC 64
SOL 4597
HAL 8
And that's it.
Thanks for your help.
Pedro.
--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil
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