Re: [gmx-users] topology of HEO compound in .rtp for G96 ff

Justin A. Lemkul Thu, 21 May 2009 11:40:21 -0700


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 areattempting to use. If this is some sort of HEME derivative, as it appears, youcan probably verify much of the topology, since HEME exists in the .rtp file forall 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 tojustify 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 9O11 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 19C13 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_34FE NB gb_34FE NC gb_34FE ND gb_34NA C1A gb_13NA C4A gb_13NB C1B gb_13NB C4B gb_13NC C1C gb_13NC C4C gb_13ND C1D gb_13ND C4D gb_13CHA C1A gb_16CHA C4D gb_16C1A C2A gb_16C2A C3A gb_16C2A CAA gb_26C3A C4A gb_16C3A CMA gb_26C4A CHB gb_16CAA CBA gb_26CBA CGA gb_26CGA O1A gb_5CGA O2A gb_5CHB C1B gb_16C1B C2B gb_16C2B C3B gb_16C2B CMB gb_26C3B C4B gb_16C4B CHC gb_16CHC C1C gb_16C1C C2C gb_16C2C C3C gb_16C2C CMC gb_26C3C C4C gb_16C3C CAC gb_26C4C CHD gb_16CAC CBC gb_11CHD C1D gb_16C1D C2D gb_16C2D C3D gb_16C2D CMD gb_26C3D C4D gb_16C3D CAD gb_26CAD CBD gb_26CBD CGD gb_26CGD O1D gb_5CGD O2D gb_5C3B C11 gb_26C11 O11 gb_4C11 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 C11NB 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 C11C1B CHC
  C2B   CHC
  C3B   C1C
  C4B   CMB
  C4B   C2C
CMB C11C11 CHCCHC 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_1NB FE NC ga_1NC FE ND ga_1NA FE ND ga_1NA FE NC ga_1 ; NR(heme) - FE - NR(heme) 100NB FE ND ga_1 ; NR(heme) - FE - NR(heme) 100FE NA C1A ga_35FE NA C4A ga_35C1A NA C4A ga_5FE NB C1B ga_35FE NB C4B ga_35C1B NB C4B ga_5FE NC C1C ga_35FE NC C4C ga_35C1C NC C4C ga_5FE ND C1D ga_35FE ND C4D ga_35C1D ND C4D ga_5C1A CHA C4D ga_36NA C1A CHA ga_32NA C1A C2A ga_14CHA C1A C2A ga_37C1A C2A C3A ga_6C1A C2A CAA ga_36C3A C2A CAA ga_36C2A C3A C4A ga_6C2A C3A CMA ga_36C4A C3A CMA ga_36NA C4A C3A ga_14NA C4A CHB ga_32C3A C4A CHB ga_37C2A CAA CBA ga_14CAA CBA CGA ga_14CBA CGA O1A ga_21CBA CGA O2A ga_21O1A CGA O2A ga_37C4A CHB C1B ga_36NB C1B CHB ga_32NB C1B C2B ga_14CHB C1B C2B ga_37C1B C2B C3B ga_6C1B C2B CMB ga_36C3B C2B CMB ga_36C2B C3B C4B ga_6NB C4B C3B ga_14NB C4B CHC ga_32C3B C4B CHC ga_37C4B CHC C1C ga_36NC C1C CHC ga_32NC C1C C2C ga_14CHC C1C C2C ga_37C1C C2C C3C ga_6C1C C2C CMC ga_36C3C C2C CMC ga_36C2C C3C C4C ga_6C2C C3C CAC ga_36C4C C3C CAC ga_36NC C4C C3C ga_14NC C4C CHD ga_32C3C C4C CHD ga_37C3C CAC CBC ga_36C4C CHD C1D ga_36ND C1D CHD ga_32ND C1D C2D ga_14CHD C1D C2D ga_37C1D C2D C3D ga_6C1D C2D CMD ga_36C3D C2D CMD ga_36C2D C3D C4D ga_6C2D C3D CAD ga_36C4D C3D CAD ga_36ND C4D CHA ga_32ND C4D C3D ga_14CHA C4D C3D ga_37C3D CAD CBD ga_14CAD CBD CGD ga_14CBD CGD O1D ga_21CBD CGD O2D ga_21O1D CGD O2D ga_37C3B 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 120C2B C3B C11 ga_36 ; X(noH) - 5-ring 100C4B C3B C11 ga_36 ; X(noH) - 5-ring 100C11 C12 C13 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C12 C13 C14 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C13 C14 C15 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C14 C15 C16 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C14 C15 C17 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C16 C15 C17 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C15 C17 C18 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C17 C18 C19 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C18 C19 C20 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C19 C20 C21 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C19 C20 C22 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C21 C20 C22 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C20 C22 C23 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C22 C23 C24 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C23 C24 C25 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C24 C25 C26 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C24 C25 C27 ga_14 ; CHn - CHn - C, CHn, OA, NR, NT, NL 110C26 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_3FE C1B C4B NB gi_3FE C1C C4C NC gi_3FE C1D C4D ND gi_3CHA NA C2A C1A gi_1CHB NA C3A C4A gi_1CHB NB C2B C1B gi_1CHC NB C3B C4B gi_1CHC NC C2C C1C gi_1CHD NC C3C C4C gi_1CHD ND C2D C1D gi_1CHA ND C3D C4D gi_1C2A C1A C3A CAA gi_1C3A C2A C4A CMA gi_1C2B C1B C3B CMB gi_1 ; planar groups 40C3B C2B C4B C11 gi_1 ; planar groups 40C2C C1C C3C CMC gi_1C3C C2C C4C CAC gi_1C2D C1D C3D CMD gi_1C3D C2D C4D CAD gi_1CBA O1A O2A CGA gi_1CBD O1D O2D CGD gi_1NA C1A C2A C3A gi_1C1A C2A C3A C4A gi_1C2A C3A C4A NA gi_1C1A NA C4A C3A gi_1C2A C1A NA C4A gi_1NB C1B C2B C3B gi_1C1B C2B C3B C4B gi_1NB C4B C3B C2B gi_1C4B NB C1B C2B gi_1C1B NB C4B C3B gi_1NC C1C C2C C3C gi_1C1C C2C C3C C4C gi_1NC C4C C3C C2C gi_1C4C NC C1C C2C gi_1C1C NC C4C C3C gi_1ND C1D C2D C3D gi_1C1D C2D C3D C4D gi_1ND C4D C3D C2D gi_1C4D ND C1D C2D gi_1C1D ND C4D C3D gi_1C11 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_5C4A CHB C1B NB gd_5NB C4B CHC C1C gd_5C4B CHC C1C NC gd_5NC C4C CHD C1D gd_5C4C CHD C1D ND gd_5ND C4D CHA C1A gd_5C4D CHA C1A NA gd_5C1A C2A CAA CBA gd_20C2A CAA CBA CGA gd_17CAA CBA CGA O1A gd_20C2C C3C CAC CBC gd_3C2D C3D CAD CBD gd_20C3D CAD CBD CGD gd_17CAD CBD CGD O1D gd_20ND 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- 1.4C26 C25 C24 C23 gd_17 ; -CHn,SI-CHn- 1.4C25 C24 C23 C22 gd_17 ; -CHn,SI-CHn- 1.4C24 C23 C22 C20 gd_17 ; -CHn,SI-CHn- 1.4C23 C22 C20 C19 gd_17 ; -CHn,SI-CHn- 1.4C22 C20 C19 C18 gd_17 ; -CHn,SI-CHn- 1.4C21 C20 C19 C18 gd_17 ; -CHn,SI-CHn- 1.4C20 C19 C18 C17 gd_17 ; -CHn,SI-CHn- 1.4C19 C18 C17 C15 gd_17 ; -CHn,SI-CHn- 1.4C18 C17 C15 C14 gd_17 ; -CHn,SI-CHn- 1.4C17 C15 C14 C13 gd_17 ; -CHn,SI-CHn- 1.4C16 C15 C14 C13 gd_17 ; -CHn,SI-CHn- 1.4C15 C14 C13 C12 gd_17 ; -CHn,SI-CHn- 1.4C14 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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Re: [gmx-users] topology of HEO compound in .rtp for G96 ff

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