[gmx-users] Label of the atoms in ffoplsaabon.itp

[Erik Lindahl]

Hi,


On Aug 3, 2006, at 1:51 PM, Eudes Fileti wrote:

> Dear Gmx users:
> I am a new user and I have some questions
> Somebody could say me what it means the index at atoms in the  
> ffoplsaabon.itp file (a fragment of file
> is gave bellow).
> Some are obvious (OH, is oxygen bonden to hydrogen and HO is a  
> hydrogen bonded to oxygen)
> but definitively I dont know what type of bond makes the carbon  
> atoms like C_2, C_3 or C *.
> I cant find this issue at manual so forgive me for the basic question.
>

They are just names, and thus not further explained in the manual :-)

The early versions of OPLS started from the Amber bonded terms and  
then recalculated nonbonded interactions, charges, and torsions.

As the force field has evolved, such that e.g. carbon atoms that  
previously had identical interactions ("C") now differ in some cases,  
particularly torsions.

Since we use the bonded atom types to specify the torsion, we need to  
use different names for them. So, C_1 through C_4 are essentially  
variants of C.

Cheers,

Erik



> Thank you
> eef
>
> ; Some esoteric OPLS atomtypes are not freely available (or  
> depreciated).
> ; Interaction types involving these have been commented out.
>
> [ bondtypes ]
> ; i    j  func       b0          kb
>   OW    HW      1    0.09572   502080.0   ; For TIP4F Water - wlj 1/98
>   OW    LP      1    0.01750   753120.0   ;          -idem-
>   C*    HC      1    0.10800   284512.0   ;
>   C     C3      1    0.15220   265265.6   ; END
>   C_2   C3      1    0.15220   265265.6   ; END
>   C_3   C3      1    0.15220   265265.6   ; END
>   C     CA      1    0.14900   334720.0   ; wlj 8/97
>   C_2   CA      1    0.14900   334720.0   ; wlj 8/97
>   C_3   CA      1    0.14900   334720.0   ; wlj 8/97
>   C     CB      1    0.14190   374049.6    ; GUA
>   C_2   CB      1    0.14190   374049.6   ; GUA
>   C_3   CB      1    0.14190   374049.6   ; GUA
>   C     CM      1    0.14440   343088.0   ; THY
>   C_2   CM      1    0.14440   343088.0   ; THY
>   C_3   CM      1    0.14440   343088.0   ; THY
>   C     CS      1    0.14900   334720.0   ;
>   C_2   CS      1    0.14900   334720.0   ;
>   C_3   CS      1    0.14900   334720.0   ;
>   C     CT      1    0.15220   265265.6   ;
>   C_2   CT      1    0.15220   265265.6   ;
>   C_3   CT      1    0.15220   265265.6   ;
>   C     CT_2    1    0.15220   265265.6   ; AA Calpha
>   C_3   CT_2    1    0.15220   265265.6   ; AA C-term
>   NO    ON      1    0.12250   460240.0    ; wlj nitro
>   CS    CW      1    0.13670   456892.8   ; wj/nm
>   CS    CS      1    0.14240   392459.2   ; -idem-
>   CS    CB      1    0.14240   392459.2   ; -idem-
>   CS    HA      1    0.10800   307105.6   ; -idem-
>   CU    NB      1    0.13200   343088.0   ; -idem-
>   CU    CA      1    0.14210   392459.2   ; -idem-
>   CU    HA      1    0.10800   307105.6   ; -idem-
>   NA    NB      1    0.13490   334720.0   ; -idem-
>   OS    NB      1    0.13990   386601.6   ; -idem-
>   OS    CR      1    0.13570   386601.6   ; -idem-
>   C3    C3      1    0.15260   217568.0   ; Ethane
>   C!    C!      1    0.14600   322168.0   ; wlj
>   C!    CS      1    0.14600   322168.0   ; wlj
>
>
> ______________________________________
>                                       Eudes Eterno Fileti
>           Centro de Ciência Naturais e Humanas
>                         Universidade Federal do ABC
>                                   Rua Santa Adélia, 166
>                                             CEP 09210-170
>                                                skype: eefileti
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