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 <saipo...@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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