[gmx-users] grompp

[Erik Marklund]

Hi,

The preprocessor cuts away all parts of the [ atoms ] section in your 
spc.itp when you use the amber forcefield. I believe there is another 
version of spc.itp that comes with the amber port. Try using that one, 
or write your own entries in the existing file between a set of #ifdef 
_FF_AMBER … #endif. I recomend you do the former.

/Erik

leila karami skrev:
> 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
>
>
> ------------------------------------------------------------------------
>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys