[gmx-users] Fatal error, spc.itp", line 41

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> I have the following error and I could not solve it after checking all
> the possible solutions on line.
> 
> Thank you
> 
> Lin
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: toppush.c, line: 1193
> 
> Fatal error:
> [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
> 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.
> -------------------------------------------------------
> 
> 

Something in your .top is out of order.  Search the archive for the solution; 
this has been asked several times with regards to spc.itp.

-Justin

> 
> spc.itp, line 41
> [ settles ]
> ; OW    funct   doh     dhh
> 1       1       0.1     0.16330
> 
> 
> 
> 
> 
> 
> The whole 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 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
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================