[gmx-users] Regarding Na ions

[Mark Abraham]

> 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.
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> 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
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>
> Would you tell me what files,  i have to modify. Any suggestion is
> appreciated.

Mark