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

[Justin Lemkul]

On 12/31/14 10:46 AM, Shima Arasteh wrote:
> 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?

Your "ligand" is just a protein, so it is within the "Protein" default group.

-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

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