[gmx-users] topology of HEO compound in .rtp for G96 ff
Egidijus Kuprusevicius
ekuprusevicius at yahoo.com
Thu May 21 20:27:32 CEST 2009
Hello, could anyone help me and check if the topology of the HEO compound was done properly for G96 ff? Thanks in advance. I couldn't find it in the database, so I decided to try to make it manualy. Any comments would be appreciated. Or maybe does exists any programs who does the work?
[ HEO ]
[ atoms ]
FE FE 0.40000 0
NA NR -0.10000 0
NB NR -0.10000 0
NC NR -0.10000 0
ND NR -0.10000 0
CHA CH1 0.00000 1
C1A C 0.00000 2
C2A C 0.00000 2
C3A C 0.00000 2
C4A C 0.00000 2
CMA CH3 0.00000 3
CAA CH2 0.00000 4
CBA CH2 0.00000 4
CGA C 0.27000 5
O1A OM -0.63500 5
O2A OM -0.63500 5
CHB CH1 0.00000 6
C1B C 0.00000 7
C2B C 0.00000 7
C3B C 0.00000 7
C4B C 0.00000 7
CMB CH3 0.00000 8
C11 C 0.38000 9
O11 O -0.38000 9
CHC CH1 0.00000 10
C1C C 0.00000 11
C2C C 0.00000 11
C3C C 0.00000 11
C4C C 0.00000 11
CMC CH3 0.00000 12
CAC CR1 0.00000 13
CBC CH2 0.00000 13
CHD CH1 0.00000 14
C1D C 0.00000 15
C2D C 0.00000 15
C3D C 0.00000 15
C4D C 0.00000 15
CMD CH3 0.00000 16
CAD CH2 0.00000 17
CBD CH2 0.00000 17
CGD C 0.27000 18
O1D OM -0.63500 18
O2D OM -0.63500 18
C12 CH2 0.00000 19
C13 CH2 0.00000 19
C14 CH2 0.00000 20
C15 CH1 0.00000 20
C16 CH3 0.00000 20
C17 CH2 0.00000 20
C18 CH2 0.00000 21
C19 CH2 0.00000 22
C20 CH1 0.00000 22
C21 CH3 0.00000 22
C22 CH2 0.00000 22
C23 CH2 0.00000 23
C24 CH2 0.00000 24
C25 CH1 0.00000 24
C26 CH3 0.00000 24
C27 CH3 0.00000 24
[ bonds ]
FE NA gb_34
FE NB gb_34
FE NC gb_34
FE ND gb_34
NA C1A gb_13
NA C4A gb_13
NB C1B gb_13
NB C4B gb_13
NC C1C gb_13
NC C4C gb_13
ND C1D gb_13
ND C4D gb_13
CHA C1A gb_16
CHA C4D gb_16
C1A C2A gb_16
C2A C3A gb_16
C2A CAA gb_26
C3A C4A gb_16
C3A CMA gb_26
C4A CHB gb_16
CAA CBA gb_26
CBA CGA gb_26
CGA O1A gb_5
CGA O2A gb_5
CHB C1B gb_16
C1B C2B gb_16
C2B C3B gb_16
C2B CMB gb_26
C3B C4B gb_16
C4B CHC gb_16
CHC C1C gb_16
C1C C2C gb_16
C2C C3C gb_16
C2C CMC gb_26
C3C C4C gb_16
C3C CAC gb_26
C4C CHD gb_16
CAC CBC gb_11
CHD C1D gb_16
C1D C2D gb_16
C2D C3D gb_16
C2D CMD gb_26
C3D C4D gb_16
C3D CAD gb_26
CAD CBD gb_26
CBD CGD gb_26
CGD O1D gb_5
CGD O2D gb_5
C3B C11 gb_26
C11 O11 gb_4
C11 C12 gb_26 ; C, CHn - C, CHn 800
C12 C13 gb_26 ; C, CHn - C, CHn 800
C13 C14 gb_26 ; C, CHn - C, CHn 800
C14 C15 gb_26 ; C, CHn - C, CHn 800
C15 C16 gb_26 ; C, CHn - C, CHn 800
C15 C17 gb_26 ; C, CHn - C, CHn 800
C17 C18 gb_26 ; C, CHn - C, CHn 800
C18 C19 gb_26 ; C, CHn - C, CHn 800
C19 C20 gb_26 ; C, CHn - C, CHn 800
C20 C21 gb_26 ; C, CHn - C, CHn 800
C20 C22 gb_26 ; C, CHn - C, CHn 800
C22 C23 gb_26 ; C, CHn - C, CHn 800
C23 C24 gb_26 ; C, CHn - C, CHn 800
C24 C25 gb_26 ; C, CHn - C, CHn 800
C25 C26 gb_26 ; C, CHn - C, CHn 800
C25 C27 gb_26 ; C, CHn - C, CHn 800
[ exclusions ]
; ai aj
FE CHA
FE C2A
FE C3A
FE CHB
FE C2B
FE C3B
FE CHC
FE C2C
FE C3C
FE CHD
FE C2D
FE C3D
NA CMA
NA CAA
NA C1B
NA C4B
NA C1C
NA C4C
NA C1D
NA C4D
NB C1A
NB C4A
NB CMB
NB C11
NB C1C
NB C4C
NB C1D
NB C4D
NC C1A
NC C4A
NC C1B
NC C4B
NC CMC
NC CAC
NC C1D
NC C4D
ND C1A
ND C4A
ND C1B
ND C4B
ND C1C
ND C4C
ND CMD
ND CAD
CHA C3A
CHA C4A
CHA CAA
CHA C1D
CHA C2D
CHA CAD
C1A CMA
C1A CHB
C1A C3D
C2A CHB
C3A C1B
C4A CAA
C4A C2B
CMA CAA
CMA CHB
CHB C3B
CHB C4B
CHB CMB
C1B C11
C1B CHC
C2B CHC
C3B C1C
C4B CMB
C4B C2C
CMB C11
C11 CHC
CHC C3C
CHC C4C
CHC CMC
C1C CAC
C1C CHD
C2C CHD
C3C C1D
C4C CMC
C4C C2D
CMC CAC
CAC CHD
CHD C3D
CHD C4D
CHD CMD
C1D CAD
C4D CMD
CMD CAD
[ angles ]
; ai aj ak gromos type
NA FE NB ga_1
NB FE NC ga_1
NC FE ND ga_1
NA FE ND ga_1
NA FE NC ga_1 ; NR(heme) - FE - NR(heme) 100
NB FE ND ga_1 ; NR(heme) - FE - NR(heme) 100
FE NA C1A ga_35
FE NA C4A ga_35
C1A NA C4A ga_5
FE NB C1B ga_35
FE NB C4B ga_35
C1B NB C4B ga_5
FE NC C1C ga_35
FE NC C4C ga_35
C1C NC C4C ga_5
FE ND C1D ga_35
FE ND C4D ga_35
C1D ND C4D ga_5
C1A CHA C4D ga_36
NA C1A CHA ga_32
NA C1A C2A ga_14
CHA C1A C2A ga_37
C1A C2A C3A ga_6
C1A C2A CAA ga_36
C3A C2A CAA ga_36
C2A C3A C4A ga_6
C2A C3A CMA ga_36
C4A C3A CMA ga_36
NA C4A C3A ga_14
NA C4A CHB ga_32
C3A C4A CHB ga_37
C2A CAA CBA ga_14
CAA CBA CGA ga_14
CBA CGA O1A ga_21
CBA CGA O2A ga_21
O1A CGA O2A ga_37
C4A CHB C1B ga_36
NB C1B CHB ga_32
NB C1B C2B ga_14
CHB C1B C2B ga_37
C1B C2B C3B ga_6
C1B C2B CMB ga_36
C3B C2B CMB ga_36
C2B C3B C4B ga_6
NB C4B C3B ga_14
NB C4B CHC ga_32
C3B C4B CHC ga_37
C4B CHC C1C ga_36
NC C1C CHC ga_32
NC C1C C2C ga_14
CHC C1C C2C ga_37
C1C C2C C3C ga_6
C1C C2C CMC ga_36
C3C C2C CMC ga_36
C2C C3C C4C ga_6
C2C C3C CAC ga_36
C4C C3C CAC ga_36
NC C4C C3C ga_14
NC C4C CHD ga_32
C3C C4C CHD ga_37
C3C CAC CBC ga_36
C4C CHD C1D ga_36
ND C1D CHD ga_32
ND C1D C2D ga_14
CHD C1D C2D ga_37
C1D C2D C3D ga_6
C1D C2D CMD ga_36
C3D C2D CMD ga_36
C2D C3D C4D ga_6
C2D C3D CAD ga_36
C4D C3D CAD ga_36
ND C4D CHA ga_32
ND C4D C3D ga_14
CHA C4D C3D ga_37
C3D CAD CBD ga_14
CAD CBD CGD ga_14
CBD CGD O1D ga_21
CBD CGD O2D ga_21
O1D CGD O2D ga_37
C3B C11 O11 ga_29 ; O - C - CHn, C 120
C3B C11 C12 ga_29 ; O - C - CHn, C 120
C12 C11 O11 ga_29 ; O - C - CHn, C 120
C2B C3B C11 ga_36 ; X(noH) - 5-ring 100
C4B C3B C11 ga_36 ; X(noH) - 5-ring 100
C11 C12 C13 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C12 C13 C14 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C13 C14 C15 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C14 C15 C16 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C14 C15 C17 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C16 C15 C17 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C15 C17 C18 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C17 C18 C19 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C18 C19 C20 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C19 C20 C21 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C19 C20 C22 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C21 C20 C22 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C20 C22 C23 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C22 C23 C24 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C23 C24 C25 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C24 C25 C26 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C24 C25 C27 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
C26 C25 C27 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110
[ impropers ]
; ai aj ak al gromos type
FE C1A C4A NA gi_3
FE C1B C4B NB gi_3
FE C1C C4C NC gi_3
FE C1D C4D ND gi_3
CHA NA C2A C1A gi_1
CHB NA C3A C4A gi_1
CHB NB C2B C1B gi_1
CHC NB C3B C4B gi_1
CHC NC C2C C1C gi_1
CHD NC C3C C4C gi_1
CHD ND C2D C1D gi_1
CHA ND C3D C4D gi_1
C2A C1A C3A CAA gi_1
C3A C2A C4A CMA gi_1
C2B C1B C3B CMB gi_1 ; planar groups 40
C3B C2B C4B C11 gi_1 ; planar groups 40
C2C C1C C3C CMC gi_1
C3C C2C C4C CAC gi_1
C2D C1D C3D CMD gi_1
C3D C2D C4D CAD gi_1
CBA O1A O2A CGA gi_1
CBD O1D O2D CGD gi_1
NA C1A C2A C3A gi_1
C1A C2A C3A C4A gi_1
C2A C3A C4A NA gi_1
C1A NA C4A C3A gi_1
C2A C1A NA C4A gi_1
NB C1B C2B C3B gi_1
C1B C2B C3B C4B gi_1
NB C4B C3B C2B gi_1
C4B NB C1B C2B gi_1
C1B NB C4B C3B gi_1
NC C1C C2C C3C gi_1
C1C C2C C3C C4C gi_1
NC C4C C3C C2C gi_1
C4C NC C1C C2C gi_1
C1C NC C4C C3C gi_1
ND C1D C2D C3D gi_1
C1D C2D C3D C4D gi_1
ND C4D C3D C2D gi_1
C4D ND C1D C2D gi_1
C1D ND C4D C3D gi_1
C11 C3B C12 O11 gi_1 ; planar groups 40
C3B C4B C2B C11 gi_1 ; planar groups 40
C15 C17 C16 C14 gi_2 ; tetrahedral centres 80
C20 C22 C21 C19 gi_2 ; tetrahedral centres 80
C25 C27 C26 C24 gi_2 ; tetrahedral centres 80
[ dihedrals ]
; ai aj ak al gromos type
NA C4A CHB C1B gd_5
C4A CHB C1B NB gd_5
NB C4B CHC C1C gd_5
C4B CHC C1C NC gd_5
NC C4C CHD C1D gd_5
C4C CHD C1D ND gd_5
ND C4D CHA C1A gd_5
C4D CHA C1A NA gd_5
C1A C2A CAA CBA gd_20
C2A CAA CBA CGA gd_17
CAA CBA CGA O1A gd_20
C2C C3C CAC CBC gd_3
C2D C3D CAD CBD gd_20
C3D CAD CBD CGD gd_17
CAD CBD CGD O1D gd_20
ND FE NA C1A 0 0 4
NA FE NB C1B 0 0 4
NB FE NC C1C 0 0 4
NC FE ND C1D 0 0 4
C2B C3B C11 O11 gd_20 ; -CHn-C,NR (ring), CR1- 0.24
C3B C11 C12 C13 gd_20 ; -CHn-C,NR (ring), CR1- 0.24
C27 C25 C24 C23 gd_17 ; -CHn,SI-CHn- 1.4
C26 C25 C24 C23 gd_17 ; -CHn,SI-CHn- 1.4
C25 C24 C23 C22 gd_17 ; -CHn,SI-CHn- 1.4
C24 C23 C22 C20 gd_17 ; -CHn,SI-CHn- 1.4
C23 C22 C20 C19 gd_17 ; -CHn,SI-CHn- 1.4
C22 C20 C19 C18 gd_17 ; -CHn,SI-CHn- 1.4
C21 C20 C19 C18 gd_17 ; -CHn,SI-CHn- 1.4
C20 C19 C18 C17 gd_17 ; -CHn,SI-CHn- 1.4
C19 C18 C17 C15 gd_17 ; -CHn,SI-CHn- 1.4
C18 C17 C15 C14 gd_17 ; -CHn,SI-CHn- 1.4
C17 C15 C14 C13 gd_17 ; -CHn,SI-CHn- 1.4
C16 C15 C14 C13 gd_17 ; -CHn,SI-CHn- 1.4
C15 C14 C13 C12 gd_17 ; -CHn,SI-CHn- 1.4
C14 C13 C12 C11 gd_17 ; -CHn,SI-CHn- 1.4
Egis
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