[gmx-users] Query regarding ligand topology

[Priya Das]

Dear All,

As per the tutorial section
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html>,
i have generated a topology for a ligand.

Atoms section is as follows:

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  LIG     CAO     1   -0.028  15.0350
     2       CH2     1  LIG     CAM     1    0.015  14.0270
     3       CH2     1  LIG     CAK     1    0.013  14.0270
     4       CH1     1  LIG     CAD     2    0.049  13.0190
     5       CH1     1  LIG     CAG     2   -0.025  14.0270
     6       CH1     1  LIG     CAJ     2   -0.024  14.0270
     7       CH1     1  LIG     CAF     3    0.032  14.0270
     8       CH1     1  LIG     CAC     3    0.099  13.0190
     9        NL     1  LIG     NAA     3    0.666  14.0067
    10         H     1  LIG     HA3     3   -0.030   1.0080
    11         H     1  LIG     HAA     3   -0.030   1.0080
    12       CH1     1  LIG     CAB     3    0.099  13.0190
    13       CH1     1  LIG     CAE     3    0.033  14.0270
    14       CH1     1  LIG     CAI     3    0.032  14.0270
    15       CH1     1  LIG     CAH     3    0.099  13.0190
    16       CH2     1  LIG     CAL     4    0.014  14.0270
    17       CH2     1  LIG     CAN     4    0.014  14.0270
    18       CH3     1  LIG     CAP     4   -0.028  15.0350

In the tutorial section, it is indicated about some mistakes in charge
groups.
How to identify if there is any mistake in this file?

-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala