[gmx-users] Charge grps and cut-off

[Sai Pooja]

This is the arginine entry in the rtp file. It assigns 12 atoms to charge
grp 3.

[ ARG ]
 [ atoms ]
        N       NH1     -0.47   0
        HN      H       0.31    0
        CA      CT1     0.07    0
        HA      HB      0.09    0
        CB      CT2     -0.18   1
        HB1     HA      0.09    1
        HB2     HA      0.09    1
        CG      CT2     -0.18   2
        HG1     HA      0.09    2
        HG2     HA      0.09    2
        CD      CT2     0.20    3
        HD1     HA      0.09    3
        HD2     HA      0.09    3
        NE      NC2     -0.70   3
        HE      HC      0.44    3
        CZ      C       0.64    3
        NH1     NC2     -0.80   3
        HH11    HC      0.46    3
        HH12    HC      0.46    3
        NH2     NC2     -0.80   3
        HH21    HC      0.46    3
        HH22    HC      0.46    3
        C       C       0.51    4
        O       O       -0.51   4


On Sat, Jul 17, 2010 at 9:17 AM, Sai Pooja <saipooja at gmail.com> wrote:

> A charge grp consisting of 12 atoms is created from Arginine residues in my
> topology file.
>
> ; residue  14 ARG rtp ARG  q +1.0
>    476        NH1     14    ARG      N    150      -0.47     14.007   ;
> qtot -3.47
>    477          H     14    ARG     HN    150       0.31      1.008   ;
> qtot -3.16
>    478        CT1     14    ARG     CA    150       0.07     12.011   ;
> qtot -3.09
>    479         HB     14    ARG     HA    150       0.09      1.008   ;
> qtot -3
>    480        CT2     14    ARG     CB    151      -0.18     12.011   ;
> qtot -3.18
>    481         HA     14    ARG    HB1    151       0.09      1.008   ;
> qtot -3.09
>    482         HA     14    ARG    HB2    151       0.09      1.008   ;
> qtot -3
>    483        CT2     14    ARG     CG    152      -0.18     12.011   ;
> qtot -3.18
>    484         HA     14    ARG    HG1    152       0.09      1.008   ;
> qtot -3.09
>    485         HA     14    ARG    HG2    152       0.09      1.008   ;
> qtot -3
>    486        CT2     14    ARG     CD    153        0.2     12.011   ;
> qtot -2.8
>    487         HA     14    ARG    HD1    153       0.09      1.008   ;
> qtot -2.71
>    488         HA     14    ARG    HD2    153       0.09      1.008   ;
> qtot -2.62
>    489        NC2     14    ARG     NE    153       -0.7     14.007   ;
> qtot -3.32
>    490         HC     14    ARG     HE    153       0.44      1.008   ;
> qtot -2.88
>    491          C     14    ARG     CZ    153       0.64     12.011   ;
> qtot -2.24
>    492        NC2     14    ARG    NH1    153       -0.8     14.007   ;
> qtot -3.04
>    493         HC     14    ARG   HH11    153       0.46      1.008   ;
> qtot -2.58
>    494         HC     14    ARG   HH12    153       0.46      1.008   ;
> qtot -2.12
>    495        NC2     14    ARG    NH2    153       -0.8     14.007   ;
> qtot -2.92
>    496         HC     14    ARG   HH21    153       0.46      1.008   ;
> qtot -2.46
>    497         HC     14    ARG   HH22    153       0.46      1.008   ;
> qtot -2
>    498          C     14    ARG      C    154       0.51     12.011   ;
> qtot -1.49
>    499          O     14    ARG      O    154      -0.51     15.999   ;
> qtot -2
>
> See charge group 153. It has 12 atoms. This is true for all Arginine
> residues. It seems that charge groups must have an integer net-charge. As
> you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge
> becomes an integer.
>
> One option would be to manually make them. In this case, I could simply
> breakdown this particular charge grp into 2 smaller chargegrps but I am sure
> if that would be consistent with the forcefield and not sure if it would be
> possible to set the net charge to an integral value to an integer for the
> smaller charge groups.
> Also, is there an alternate way by changing the Cut-off?
>
> Any thoughts?
> Pooja
>
>
>
> Pooja
>
>


-- 
Quaerendo Invenietis-Seek and you shall discover.
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