[gmx-users] Query regarding ligand topology

[Justin Lemkul]

On 12/19/14 6:31 AM, Priya Das wrote:
> 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?
>

Identifying errors depends on how well you know the principles of the force 
field.  Charge groups should never be more than 3-4 atoms.  Given that charge 
group 3 encompasses half the molecule, you can tell that there was likely a 
problem in assigning charges to those atoms.  Since Gromos force fields are 
united-atom, aliphatic groups by definition are uncharged.  All of your CH3, 
CH2, and CH1 groups have charges (some CH1 may need a charge depending on what 
it's connected to, but that's up to you to decide).  Pretty much all of the 
charges you have are suspicious.  Compare against known functional groups in the 
force field based on chemical similarity.  Your molecule looks quite simple to 
fix up.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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