[gmx-users] Regarding Na ions

[Yang Ye]

Open ions.itp and check what does Sodium is called for OPLSAA force field.

On 7/5/2007 10:22 PM, naga raju wrote:
> 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"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> Mixture of  POPE and POPG lipid bilayer in 3:1 ratio
>
> [ 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.
>
>                                                              Thank you 
> in advance.
>
>                                                                                                                
> with regards,
>                                                                                                           
>            Nagaraju
>
>
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