Dear Mark,
I put #include "disre.itp" at the end of making a hybrid [molecule] section
as you've suggested, 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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