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

[Victor Ma]

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