[gmx-users] Define a new group for protein-ligand complex system

[Shima Arasteh]

Hi,
Dear users,
I am trying to define a new group for the ligand in a ligand-protein
system. According to the protein-ligand complex tutorial existed in
documentation, I made my ligand.itp file, also I included it in top
file:
Ligand.itp contains:

[ moleculetype ]
; Name            nrexcl
HH    3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
; residue   1 LYS rtp LYS  q +2.0
     1        NH3      1    LYS      N      1       -0.3     14.007
; qtot -0.3
     2         HC      1    LYS     H1      2       0.33      1.008
; qtot 0.03
.
.
.
.
.
  214   213   215   216     2

[ cmap ]
;  ai    aj    ak    al    am funct
   23    25    27    47    49     1
   47    49    51    71    73     1
   71    73    75    95    97     1
   95    97    99   117   119     1
  117   119   121   141   143     1
  141   143   145   165   167     1
  165   167   169   189   191     1

And topol.top:
.
.
.
.
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand topology
#include "ligand.itp"

; Include water topology
#include "./charmm36-modified.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "./charmm36-modified.ff/ions.itp"

[ system ]
; Name
HH_protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
HH                  1
SOL         7901

After building the box, I filled it with sol molecules. For
neutralization, I selected sol molecules to be replaced by a few ions.
It is ok and I dont want to replace the ions with any other option.
But, I expect to see HH among other options as well, however it does
not exist. I thought of a problem with my new defined group (ligand
group). It seems that is not recognized as a separate group.

Would you please let me you know your suggestions?
I appreciate that.

Shima