[gmx-users] ligand-protein distance restraint

[Pathumwadee Intharathep]

Dear gmx-user,
 
I put #include "disre.itp"   at the end of making a hybrid [molecule] section as mark's suggestion, I got the same error after grompp. 

  
“Fatal error: [ file "../disre.itp", line 2 ]: 
             Atom index (195) in distance_restraints out of bounds (1-1)” 
 
;       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 "rimq1_top.itp"              ;ligand topology file 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
#include "disre.itp"   
------------------------------------------ 
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 

I also try to merge the ligand into protein topology by using pdb2gmx but it can not file the forcefield for ligand. 
  

 Thanks so much
 
pathum



      
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