[gmx-users] The sum of the two largest charge group radii is larger than rlist

[pratibha]

Hi Dr. Vitaly

My protein is not defined as a single charge group (if I understand
correctly). All residues have their respective charges. First few lines of
my topology file are as follows:

; Name            nrexcl
Protein_chain_A     3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB   
chargeB      massB
; residue   1 LYS rtp LYSH q +2.0
     1         NL      1    LYS      N      1      0.129    14.0067   ; qtot
0.129
     2          H      1    LYS     H1      1      0.248      1.008   ; qtot
0.377
     3          H      1    LYS     H2      1      0.248      1.008   ; qtot
0.625
     4          H      1    LYS     H3      1      0.248      1.008   ; qtot
0.873
     5        CH1      1    LYS     CA      2      0.127     13.019   ; qtot
1
     6        CH2      1    LYS     CB      2          0     14.027   ; qtot
1
     7        CH2      1    LYS     CG      3          0     14.027   ; qtot
1
     8        CH2      1    LYS     CD      3          0     14.027   ; qtot
1
     9        CH2      1    LYS     CE      4      0.127     14.027   ; qtot
1.127
    10         NL      1    LYS     NZ      4      0.129    14.0067   ; qtot
1.256
    11          H      1    LYS    HZ1      4      0.248      1.008   ; qtot
1.504
    12          H      1    LYS    HZ2      4      0.248      1.008   ; qtot
1.752
    13          H      1    LYS    HZ3      4      0.248      1.008   ; qtot
2
    14          C      1    LYS      C      5       0.45     12.011   ; qtot
2.45
    15          O      1    LYS      O      5      -0.45    15.9994   ; qtot
2
 
I apologize if I did not get the question right. Help me resolve the
problem,
Thanks in advance.

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