[gmx-users] query regarding automated topology builder and repository

[Sanchaita Rajkhowa]

Dear all,
    I would like to know if automated topology builder and repository
server "
http://compbio.biosci.uq.edu.au/atb/index.py?tab=existing_tab&nocache=836
" gives the correct topology for ligands? For e.g. I have to build
topology for triclosan and it is present in this repository.
    But the total charge on the charge group is not 0.00. For e.g.
-------------------------------------------------------------------------

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1     H    1    _NNX     H7    1    0.463   1.0080
    2    OA    1    _NNX    O16    1   -0.558  15.9994      ; -0.095
    3    OE    1    _NNX     O7    2   -0.395  15.9994
    4    HC    1    _NNX     H4    2    0.191   1.0080
    5     C    1    _NNX    C12    2    0.225  12.0110
    6     C    1    _NNX     C8    2   -0.312  12.0110
    7     C    1    _NNX     C7    2    0.291  12.0110      ; -0.000
    8    CL    1    _NNX   CL14    3   -0.080  35.4530
    9     C    1    _NNX     C4    3   -0.277  12.0110
   10     C    1    _NNX     C3    3    0.552  12.0110      ;  0.195
   11    CL    1    _NNX   CL15    4   -0.093  35.4530
   12     C    1    _NNX     C6    4   -0.163  12.0110
   13     C    1    _NNX     C5    4    0.138  12.0110
   14    HC    1    _NNX     H3    4    0.118   1.0080      ;  0.000
   15     C    1    _NNX     C2    5   -0.442  12.0110
   16    HC    1    _NNX     H2    5    0.207   1.0080
   17    HC    1    _NNX     H1    5    0.138   1.0080
   18     C    1    _NNX     C1    5    0.097  12.0110      ;  0.000
   19    HC    1    _NNX     H6    6    0.152   1.0080
   20     C    1    _NNX    C11    6   -0.252  12.0110      ; -0.100
   21    HC    1    _NNX     H5    7    0.157   1.0080
   22    CL    1    _NNX   CL17    7   -0.096  35.4530
   23     C    1    _NNX    C10    7   -0.004  12.0110
   24     C    1    _NNX     C9    7   -0.057  12.0110      ; -0.000
; total charge of the molecule:  -0.000

---------------------------------------------------------------
Do I need to modify it before doing the simulation or use it as it is?

Thanks.
Sanchaita.
-- 
SANCHAITA RAJKHOWA,
Research Scholar,
C/O Prof. Ramesh C. Deka,
Department of Chemical Science,
Tezpur University,
Napaam,
Tezpur-784 028


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