[gmx-users] Regarding Na ions

[Osmair Vital de Oliveira]

You can build a file, e.g. sodium.itp:

[ moleculetype ]
; Name            nrexcl
sodium            1

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
chargeB      massB
     1   opls_405      1     Na     Na      1         1     35.453   ;
qtot 1
     2   opls_405      2     Na     Na      2         1     35.453   ;
qtot 2
     2   opls_405      3     Na     Na      3         1     35.453   ;
qtot 2
     .
     .
     .

Osmair
Brazil


> > Dear gmx users,
> >                                   I am trying to neutralize lipid bilayer
> > with Na ions by using genion command:
> >  genion -f bilayer.tpr -o bilayer-Na.pdb  -np  32 -pname Na  -pq 1
> >
> > Here is my bilayer.top file
> > #include "ffoplsaa.itp"
> > #include "pope.itp"
> > #include "dpopg.itp"
> > #include "ions.itp"
>
> One of these ones should be defining a sodium ion moleculetype ... have a
> look and see what it's called there!
>
> > [ molecules ]
> > ; name    number
> > POPE      96
> > DPOP      32
> > SOL      3909
> > Na           32
> >
> > I am getiing fallowing eror.
> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> > processing topology...
> > Generated 344865 of the 344865 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 344775 of the 344865 1-4 parameter combinations
> > Excluding 3 bonded neighbours for POPE 96
> > turning all bonds into constraints...
> > Excluding 3 bonded neighbours for DPOP 32
> > turning all bonds into constraints...
> > Excluding 2 bonded neighbours for SOL 3909
> > turning all bonds into constraints...
> > Cleaning up temporary file gromppVHJgxO
> > -------------------------------------------------------
> > Program grompp, VERSION 3.3.1
> > Source code file: toppush.c, line: 1293
> >
> > Fatal error:
> > No such moleculetype Na
> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> >
> > Would you tell me what files,  i have to modify. Any suggestion is
> > appreciated.
>
> Mark
>
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