[gmx-users] Zwitterionic amino acid topology parameters in CHARMM

[rose rahmani]

Hi,

I want to use zwitterionic form of AAs in CHARMM ff. I gave structure in
Discovery studio and then use pdb2gmx to get its topology and ... files.
But the number of atoms in topol.top and also some atom's partial charges
are different from atoms and charges in aminoacids.rtp
For example, in the case of phenylalanine,
this is topology file after pdb2gmx:

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
  chargeB      massB
; residue   1 PHE rtp PHE  q  0.0
     1        NH3      1    PHE      N      1       -0.3     14.007   ;
qtot -0.3
     2         HC      1    PHE     H1      2       0.33      1.008   ;
qtot 0.03
     3         HC      1    PHE     H2      3       0.33      1.008   ;
qtot 0.36
     4         HC      1    PHE     H3      4       0.33      1.008   ;
qtot 0.69
     5        CT1      1    PHE     CA      5       0.21     12.011   ;
qtot 0.9
     6         HB      1    PHE     HA      6        0.1      1.008   ;
qtot 1
     7        CT2      1    PHE     CB      7      -0.18     12.011   ;
qtot 0.82
     8         HA      1    PHE    HB1      8       0.09      1.008   ;
qtot 0.91
     9         HA      1    PHE    HB2      9       0.09      1.008   ;
qtot 1
    10         CA      1    PHE     CG     10          0     12.011   ;
qtot 1
    11         CA      1    PHE    CD1     11     -0.115     12.011   ;
qtot 0.885
    12         HP      1    PHE    HD1     12      0.115      1.008   ;
qtot 1
    13         CA      1    PHE    CE1     13     -0.115     12.011   ;
qtot 0.885
    14         HP      1    PHE    HE1     14      0.115      1.008   ;
qtot 1
    15         CA      1    PHE     CZ     15     -0.115     12.011   ;
qtot 0.885
    16         HP      1    PHE     HZ     16      0.115      1.008   ;
qtot 1
    17         CA      1    PHE    CD2     17     -0.115     12.011   ;
qtot 0.885
    18         HP      1    PHE    HD2     18      0.115      1.008   ;
qtot 1
    19         CA      1    PHE    CE2     19     -0.115     12.011   ;
qtot 0.885
    20         HP      1    PHE    HE2     20      0.115      1.008   ;
qtot 1
    21         CC      1    PHE      C     21       0.34     12.011   ;
qtot 1.34
    22         OC      1    PHE    OT1     22      -0.67     15.999   ;
qtot 0.67
    23         OC      1    PHE    OT2     23      -0.67     15.999   ;
qtot 0

and this is .rtp file for PHE:

[ PHE ]
 [ atoms ]
        N       NH1     -0.47   0
        HN      H       0.31    1
        CA      CT1     0.07    2
        HA      HB      0.09    3
        CB      CT2     -0.18   4
        HB1     HA      0.09    5
        HB2     HA      0.09    6
        CG      CA      0.00    7
        CD1     CA      -0.115  8
        HD1     HP      0.115   9
        CE1     CA      -0.115  10
        HE1     HP      0.115   11
        CZ      CA      -0.115  12
        HZ      HP      0.115   13
        CD2     CA      -0.115  14
        HD2     HP      0.115   15
        CE2     CA      -0.115  16
        HE2     HP      0.115   17
        C       C       0.51    18
        O       O       -0.51   19
so as you see there O and 2 H more...  . I know that's because of COO group
and HH.. but which of them are the real structure of zwitterionic form of
 amino acid in force field? are both true? I would be appreciated if you
can help me.

Best