Pathumwadee Intharathep wrote:
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"
You can avoid the need to specify particular directories each time
through careful use of the GMXLIB environment variable, or using
"include = -I /some/dir" in your .mdp file. See
http://wiki.gromacs.org/index.php/Include_File_Mechanism
You should also refrain from using ffgmx, as it's been deprecated for
ages now.
; 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.
Distance restraints may only be intra-molecular. Thus you will need to
make a hybrid [molecule] section that includes your protein and all of
its distance-restrained ligands and #include "disre.itp" at the end of
that [molecule] section.
Mark
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