[gmx-users] ligand-protein distance restraint

[Pathumwadee Intharathep]

Dear gmx-users,
 
Do you know how to make distance restraint between ligand and protein in gromacs?
I have a chain of protein binds with 4 drugs in water-lipid box, the topology put below..


;       File 'top.top' was generated; Include forcefield parameters
;
#include "/home/bio001/02_saow/gromacs_top/jit/top/ffgmx.itp"
#include "/home/bio001/02_saow/gromacs_top/jit/popc.itp"
; Include chain topologies
#include "1add_H/0H_addH1.top"              ;protein atom 1-1615
#include "disre.itp"                                      ; distance restraint topology file
#include "rimq1_top.itp"                              ;ligand topology file atom 1-16
; Include water topology
#include "/home/bio001/02_saow/gromacs_top/jit/top/flexspc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif
; Include generic topology for ions
#include "/home/bio001/02_saow/gromacs_top/jit/top/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound        #mols
Protein_A             1
RIM                      4
POPC                  74
SOL                   3763
Cl                       8
 
------------------------------------------
detailed in "disre.itp" file is
[ distance_restraints ]
     195   1628   1   1     1   0.25 0.35 0.40 1.0
     195    563   1   1     1   0.25 0.35 0.40 1.0
     598   1644   1   1     1   0.25 0.35 0.40 1.0
     598    966   1   1     1   0.25 0.35 0.40 1.0
    1001   1660   1   1     1   0.25 0.35 0.40 1.0
    1001    369   1   1     1   0.25 0.35 0.40 1.0
    1404   1676   1   1     1   0.25 0.35 0.40 1.0
    1404    160   1   1     1   0.25 0.35 0.40 1.0

The error occur after grompp run is..
 
“Fatal error: [ file "../disre.itp", line 2 ]:
             Atom index (1628) in distance_restraints out of bounds (1-1615)”
 
It seems to be that the atoms from ligand (rimq1_top.itp) topology was not known.


My question is 
Q1: Where I should put “disre.itp” in topology file that it can recognize the atom from both protein (0H_addH1.top) and ligand (rimq1_top.itp) topology files. 

 Thanks so much
 
pathum


      
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