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urea_single_molecule.itp
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; urea.pdb.mol2_GMX.itp created by acpype (v: 2022.7.21) on Tue Oct 17 10:11:40 2023
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
hn hn 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157
c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
n n 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
[ moleculetype ]
;name nrexcl
LIG 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 hn 1 LIG H 1 0.299000 1.00800 ; qtot 0.299
2 c 1 LIG C 2 0.727100 12.01000 ; qtot 1.026
3 o 1 LIG O 3 -0.639100 16.00000 ; qtot 0.387
4 n 1 LIG N 4 -0.642000 14.01000 ; qtot -0.255
5 hn 1 LIG H1 5 0.299000 1.00800 ; qtot 0.044
6 hn 1 LIG H2 6 0.299000 1.00800 ; qtot 0.343
7 n 1 LIG N1 7 -0.642000 14.01000 ; qtot -0.299
8 hn 1 LIG H3 8 0.299000 1.00800 ; qtot 0.000
[ bonds ]
; ai aj funct r k
1 4 1 1.0129e-01 3.3740e+05 ; H - N
2 3 1 1.2183e-01 5.3363e+05 ; C - O
2 4 1 1.3789e-01 3.5782e+05 ; C - N
2 7 1 1.3789e-01 3.5782e+05 ; C - N1
4 5 1 1.0129e-01 3.3740e+05 ; N - H1
6 7 1 1.0129e-01 3.3740e+05 ; H2 - N1
7 8 1 1.0129e-01 3.3740e+05 ; N1 - H3
[ pairs ]
; ai aj funct
1 3 1 ; H - O
1 7 1 ; H - N1
3 5 1 ; O - H1
3 6 1 ; O - H2
3 8 1 ; O - H3
4 6 1 ; N - H2
4 8 1 ; N - H3
5 7 1 ; H1 - N1
[ angles ]
; ai aj ak funct theta cth
1 4 2 1 1.1755e+02 4.0417e+02 ; H - N - C
1 4 5 1 1.1795e+02 3.3137e+02 ; H - N - H1
2 4 5 1 1.1755e+02 4.0417e+02 ; C - N - H1
2 7 6 1 1.1755e+02 4.0417e+02 ; C - N1 - H2
2 7 8 1 1.1755e+02 4.0417e+02 ; C - N1 - H3
3 2 4 1 1.2305e+02 6.2091e+02 ; O - C - N
3 2 7 1 1.2305e+02 6.2091e+02 ; O - C - N1
4 2 7 1 1.1356e+02 6.1003e+02 ; N - C - N1
6 7 8 1 1.1795e+02 3.3137e+02 ; H2 - N1 - H3
[ dihedrals ] ; propers
; for gromacs 4.5 or higher, using funct 9
; i j k l func phase kd pn
1 4 2 3 9 0.00 8.36800 1 ; H- N- C- O
1 4 2 3 9 180.00 10.46000 2 ; H- N- C- O
1 4 2 7 9 180.00 10.46000 2 ; H- N- C- N1
3 2 4 5 9 0.00 8.36800 1 ; O- C- N- H1
3 2 4 5 9 180.00 10.46000 2 ; O- C- N- H1
3 2 7 6 9 0.00 8.36800 1 ; O- C- N1- H2
3 2 7 6 9 180.00 10.46000 2 ; O- C- N1- H2
3 2 7 8 9 0.00 8.36800 1 ; O- C- N1- H3
3 2 7 8 9 180.00 10.46000 2 ; O- C- N1- H3
4 2 7 6 9 180.00 10.46000 2 ; N- C- N1- H2
4 2 7 8 9 180.00 10.46000 2 ; N- C- N1- H3
5 4 2 7 9 180.00 10.46000 2 ; H1- N- C- N1
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
2 1 4 5 4 180.00 4.60240 2 ; C- H- N- H1
2 6 7 8 4 180.00 4.60240 2 ; C- H2- N1- H3
4 7 2 3 4 180.00 43.93200 2 ; N- N1- C- O