[gmx-users] topology of HEO compound in .rtp for G96 ff
Justin A. Lemkul
jalemkul at vt.edu
Thu May 21 20:38:51 CEST 2009
Egidijus Kuprusevicius wrote:
> 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?
>
It would help to know what "HEO" is, and which version of Gromos96 you are
attempting to use. If this is some sort of HEME derivative, as it appears, you
can probably verify much of the topology, since HEME exists in the .rtp file for
all the Gromos96 variants.
It is not possible to simply look at a topology and verify if it is correct.
Parameterization requires you to verify some sort of experimental observable to
justify the parameters you have assigned.
-Justin
>
> [ 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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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