[gmx-users] Wrong charge group assinment: pdb2gmx of 4.5 beta3

[Chiba Shuntaro]

Dear gmx-users,

 

New pdb2gmx seems to be strange that

the net charge of the first group (N terminal) is not decimal number.

 

I put LEU-TRP-VAL.pdb (attached file) into pdb2gmx

and chose ffG53a6 for the force field.

 

In the topol.top (attached file) obtained,

the first and second charge groups are as follows:

 

[ atoms ]
;   nr    type  resnr residue  atom cgnr  charge mass  typeB chargeB massB
; residue  33 LEU rtp LEU  q +1.0
     1  NL    33  LEU    N   1  0.129  14.0067  ; qtot 0.129
     2  H     33  LEU   H1   1  0.248   1.008   ; qtot 0.377
     3  H     33  LEU   H2   1  0.248   1.008   ; qtot 0.625
     4  H     33  LEU   H3   1  0.248   1.008   ; qtot 0.873
     5  CH1   33  LEU   CA   2  0.127  13.019   ; qtot 1
     6  CH2   33  LEU   CB   2      0  14.027   ; qtot 1

 

I am sorry if I misunderstand it.

 

Best regards,

Shuntaro
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