[gmx-users] Hydroixde Ion

[Mark Abraham]

On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
> Hello,
>
> I am new gromacs user.
> I am trying to set up a water-methanol system with few hyrdroxide ions.
>
> Since hyrdroxide ion does not already exist in gromacs database, I 
> defined the following in the .rtp file ( I am using ffG53a6)
>
> [ OH ]
>  [ atoms ]
>    OW    OW    -1.41000     0
>   HW1     H     0.41000     0
>  [ bonds ]
>    OW   HW1    gb_38
>  [ angles ]
> ;  ai    aj    ak   gromos typpe
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>  [ dihedrals ]
> ;  ai    aj    ak    al   gromos type

That's only useful for pdb2gmx when generating .top files.

> I also included OH in the .atp file ( I realise that hydroxide ion is 
> NOT an atom, its a diatomic anion, I was just trying!)

Don't. The .atp defines *atom* types.

> I ran into the error: No such moleculetype OH
>
> I further included information in the ions.itp as follows:
>
> [ moleculetype ]
> ; molname   nrexcl
> OH    1
>
> [ atoms ]
> ; id  at type  res nr   residu name at name  cg nr charge
> 1  OH 1  OH    OH  1 -1

Use two atoms, like you did for your .rtp entry.

> The genion adds the "OH"  in the .gro file and also the topol.top but 
> when I try to minimize the system using
> grompp -f minim.mdp -c 5his8_meohi_wat.gro -p topol.top -o em.tpr
> I am still running into the same error, No such moleculetype OH.

Your .top still does not have a functional [ moleculetype ] OH. You're 
probably not using the #include "ions.itp"  mechanism correctly.

Mark