[gmx-users] grompp

[leila karami]

dear justin

Fatal error:
[ file spc.itp, line 46 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.

I checked topology file and sent topology and spc.itp file. please guide me.

this is my topology file :

; Include forcefield parameters
#include "ffamber03.itp"

; Include chain topologies
#include "c_A.itp"
#include "c_B.itp"

; Include water topology
#include "spc.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 "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL              7127

this is my spc.itp file:

[ moleculetype ]
; molname    nrexcl
SOL        2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge       mass
#ifdef _FF_GROMACS
     1     OW      1    SOL     OW      1      -0.82
     2     HW      1    SOL    HW1      1       0.41
     3     HW      1    SOL    HW2      1       0.41
#endif
#ifdef _FF_GROMOS96
#ifdef HEAVY_H
     1     OW      1    SOL     OW      1      -0.82    9.95140
     2      H      1    SOL    HW1      1       0.41    4.03200
     3      H      1    SOL    HW2      1       0.41    4.03200
#else
     1     OW      1    SOL     OW      1      -0.82   15.99940
     2      H      1    SOL    HW1      1       0.41    1.00800
     3      H      1    SOL    HW2      1       0.41    1.00800
#endif
#endif
#ifdef _FF_OPLS
     1  opls_116   1    SOL     OW      1      -0.82
     2  opls_117   1    SOL    HW1      1       0.41
     3  opls_117   1    SOL    HW2      1       0.41
#endif
#ifdef _FF_CHARMM
     1     OW      1    SOL     OW      1      -0.82
     2     HW      1    SOL    HW1      1       0.41
     3     HW      1    SOL    HW2      1       0.41
#endif

#ifdef FLEXIBLE
[ bonds ]
; i    j    funct    length    force.c.
1    2    1    0.1    345000    0.1     345000
1    3    1    0.1    345000    0.1     345000

[ angles ]
; i    j    k    funct    angle    force.c.
2    1    3    1    109.47    383    109.47    383
#else
[ settles ]
; OW    funct    doh    dhh
1    1    0.1    0.16330

[ exclusions ]
1    2    3
2    1    3
3    1    2
#endif
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091103/22eccb02/attachment.html>