[gmx-users] Error in Ligand position restraints

[neha bharti]

Hello All


I am trying to perform MD for protein ligand protein complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.

I successfully performed till

 perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat

After this when I started performing energy minimization part it gives
error :

Fatal error:
[ file strong_posre.itp, line 6979 ]:
Atom index (6975) in position_restraints out of bounds (1-6974).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


I think the problem is that I have included position restraints for protein
in topology file but not includes position restraints for ligand in that
file.


when I added

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif


to my topology file it consider both protein and ligand so the number of
residue present in my position restraint file and Strong position restraint
is different.


I also check it by adding position restraint for ligand in my topology
file. but it still giving the same error.

I also check by merging position restraint file for ligand and protein but
the same error is present.


This is my topology file:

; Include forcefield parameters
#include "charmm36_lipid.ff/forcefield.itp"


; Include ligand topology
#include "lig.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
...
...
...
....

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Ligand position restraints
#ifdef POSRES
#include "posre_lig.itp"
#endif


; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif


; Include POPC chain topology
#include "popc.itp"


; Include water topology
#include "charmm36_lipid.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_lipid.ff/ions.itp"

[ system ]
; Name
Gyas ROwers Mature At Cryogenic Speed

[ molecules ]
; Compound        #mols
Protein                   1
lig                  1
POPC    128


I have also check by changing the position of lig.itp file and posre_lig
file by keeping them together like


; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand topology
#include "lig.itp"

; Ligand position restraints
#ifdef POSRES
#include "posre_lig.itp"
#endif

then it gives another error because of the change in position of ligand
topology file.

Fatal error:
Syntax error - File cyc.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes


Please Help.

Thanks in Advance

With Regards
Neha bharty