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

[Justin Lemkul]

On 5/8/14, 1:06 AM, Sanchaita Rajkhowa wrote:
>
> 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.

Charge groups do not have to be neutral, at least if you're using PME for the 
simulation.

> -------------------------------------------------------------------------
>
> [ 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?
>

Without context (i.e. which atoms are which in the actual structure), it's hard 
to judge the quality.  One thing that sticks out to me is the phenolic group; 
its charge group only contains the OH without the C, which is weird.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================