[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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