[gmx-users] Hydroixde Ion

[SHIVANGI NANGIA]

Hello,

Thanks a lot for the suggestion.

I think I made some progress but I am not there yet.

I added the following in the ions.itp file

[ moleculetype ]
; molname   nrexcl
OH    1

[ atoms ]
; id  at type  res nr   residu name at name  cg nr charge
1  OH 1  OH    OH  1  0
1  OW 1  OW    OW  1 -1


Still I ran into the same error that it could not find moleculetype OH.

Than I specifically added the following to the .top file

[ moleculetype ]
; molname   nrexcl
OH    1

[atoms]
     1         OH      1   OH     OH      1       0.21     1.008     ;
     2         OW      1   OH     OW      1      -1.21    15.99994   ;
[ bonds ]
   OW   HW1    gb_38

This helped. 
However, there is new error I am running into which says: 
Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro,
12487) does not match topology (topol.top, 12519)

I am trying to add 8 hydroxide ions in my methanol-water system.

The confusion I have is: 
The .gro file has OH but is gromacs really accounting OH as 2 atoms?  
Also, the difference (12519-12487) is greater than 8. 

Kindly help.

Thanks,
Shivangi



Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802

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

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