[gmx-users] how to apply distance restrains between a residue and an ion

[Victor Ma]

I know it might be a silly question. But can someone please help me out
here?
Thank you so so much!

Victor

On Tue, Sep 1, 2015 at 11:54 AM, Victor Ma <victordsmagift at gmail.com> wrote:

> hello all
>
> I need to apply a distance restraint between a sodium and a residue. I
> read the manual, etc, which seems to suggest adding something like below to
> the .itp file.
>
> [ distance_restraints ]
> ; ai aj type index type’ low up1 up2 fac
>   10 16 1    0     1     0.0 0.3 0.4 1.0
>   10 28 1    1     1     0.0 0.3 0.4 1.0
>
> But my protein and ions are in two separate itp file. So how do I do it?
>
> Also I have multiple sodiums, but in the SOD.itp file, there is only one line
> [ moleculetype ]
> ; name  nrexcl
> SOD          1
>
> [ atoms ]
> ; nr    type    resnr   residu  atom    cgnr    charge  mass
>      1        SOD      1      SOD    SOD      1      1.000    22.9898   ; qtot  1.000
>
> So how do I get the atom number for the specific sodium I want to restraint?
>
> Thank you so much.
>
>
> Victor
>
>
>