[gmx-users] grompp

[Justin A. Lemkul]

leila karami wrote:
> 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:
> 

Note how that in spc.itp, none of the #ifdef statements cover any of the AMBER 
force fields.  You must either create the appropriate entry, or use a water 
model that is, by default, compatible with AMBER.

-Justin

> [ 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
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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