[gmx-users] How to calculate radial distribution functions when atoms in different amino acids are named similarly

[Apramita Chand]

Dear All,
 Following is a portion of my .top file showing the naming of atoms of two
of my amino acids of my protein
 residue  22 TYR rtp TYR  q +1.0
     1         NL     22    TYR      N      1      0.129    14.0067   ;
qtot 0.129
     2          H     22    TYR     H1      1      0.248      1.008   ;
qtot 0.377
     3          H     22    TYR     H2      1      0.248      1.008   ;
qtot 0.625
     4          H     22    TYR     H3      1      0.248      1.008   ;
qtot 0.873
     5        CH1     22    TYR     CA      2      0.127     13.019   ;
qtot 1
     6        CH2     22    TYR     CB      2          0     14.027   ;
qtot 1
     7          C     22    TYR     CG      2          0     12.011   ;
qtot 1
     8          C     22    TYR    CD1      3      -0.14     12.011   ;
qtot 0.86
     9         HC     22    TYR    HD1      3       0.14      1.008   ;
qtot 1
    10          C     22    TYR    CD2      4      -0.14     12.011   ;
qtot 0.86
    11         HC     22    TYR    HD2      4       0.14      1.008   ;
qtot 1
    12          C     22    TYR    CE1      5      -0.14     12.011   ;
qtot 0.86
    13         HC     22    TYR    HE1      5       0.14      1.008   ;
qtot 1
    14          C     22    TYR    CE2      6      -0.14     12.011   ;
qtot 0.86
    15         HC     22    TYR    HE2      6       0.14      1.008   ;
qtot 1
    16          C     22    TYR     CZ      7      0.203     12.011   ;
qtot 1.203
    17         OA     22    TYR     OH      7     -0.611    15.9994   ;
qtot 0.592
    18          H     22    TYR     HH      7      0.408      1.008   ;
qtot 1
    19          C     22    TYR      C      8       0.45     12.011   ;
qtot 1.45
    20          O     22    TYR      O      8      -0.45    15.9994   ;
qtot 1
; residue  23 GLY rtp GLY  q  0.0
    21          N     23    GLY      N      9      -0.31    14.0067   ;
qtot 0.69
    22          H     23    GLY      H      9       0.31      1.008   ;
qtot 1
    23        CH2     23    GLY     CA     10          0     14.027   ;
qtot 1
    24          C     23    GLY      C     11       0.45     12.011   ;
qtot 1.45
    25          O     23    GLY      O     11      -0.45    15.9994   ;
qtot 1


As you can notice , atoms N,C,O of TYR and GLY are named similarly. So when
we calculate rdfs of the protein sites with water molecules, the index
files have to be created which may cause confusion as to which site is
referred to when we mention 'N' or 'C'.
So is re-naming the names necessary or is there a way to calculate rdfs
with the existing file?

Could different index files help? How can we create such index files for
different amino acids?

Thanking you,
yours sincerely,
Apramita Chand