[gmx-users] OPLSAA.ff

[Mark Abraham]

For example, C* is used in ffbonded.itp, which can be looked up in
ffnonbonded as opls_500, which atomtypes.atp reveals as a Trp gamma carbon.

Mark


On Sat, Jun 1, 2013 at 2:27 AM, Broadbent, Richard <
richard.broadbent09 at imperial.ac.uk> wrote:

> The conversion is in ffnonbonded.itp. However, unless you plan to modify
> the forcefield you shouldn't need this.
>
> Richard
>
> On 01/06/2013 00:57, "Hari Pandey" <harichem12 at yahoo.com> wrote:
>
> >Dear Gromacs users,
> >
> >I am a new user and I have some questions
> > I confused about indexing.  in atomtypes.atp  clearly  we can know the
> >index is for what kind of atom but  in ffbondedtype.itp there is
> >different kind of the indexing  so I confused how do i pathch the force
> >field .
> >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 *
> >Can somebody help me what represents in ffbonded.atp.
> >for example : opls_083  means S in RSR , opls_091  means CH2 in RCH2SR
> >but what type of atoms are C*, C_2, C_3 ,  CT, CM, CS, LP, CT_2, CT_3,
> >CW, NB etc.
> >
> >
> >could you please provide me idea or list for that if somebody have.
> >Thanks
> >
> >
> >In Oplsaa.ff the indexing is  as follows :
> >
> >atomtypes.atp
> >
> >
> >opls_079    1.00800  ; H(O) ALCOHOLS     JPC,90,1276 (1986)
> > opls_080   15.03500  ; CH3 IN METHANOL   JPC,90,1276 (1986)
> > opls_081   14.02700  ; CH2 IN ETHANOL    JPC,90,1276 (1986)
> > opls_082   32.06000  ; S   IN H2S        JPC,90,6379 (1986)
> > opls_083   32.06000  ; S   IN RSH        JPC,90,6379 (1986)
> > opls_084   32.06000  ; S   IN RSR        JPC,90,6379 (1986)
> > opls_085   32.06000  ; S   IN RSSR       JPC,90,6379 (1986)
> > opls_086    1.00800  ; H   IN H2S        JPC,90,6379 (1986)
> > opls_087    1.00800  ; H(S) IN RSH       JPC,90,6379 (1986)
> > opls_088   15.03500  ; CH3 IN CH3SH      JPC,90,6379 (1986)
> > opls_089   14.02700  ; CH2 IN CH3CH2SH   JPC,90,6379 (1986)
> > opls_090   15.03500  ; CH3 IN CH3SR      JPC,90,6379 (1986)
> > opls_091   14.02700  ; CH2 IN RCH2SR     JPC,90,6379 (1986
> >
> >The ffbonded.itp is as follows ; 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
> >--
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