[gmx-users] Placing anion/cation at a particular distance from peptide

[Mark Abraham]

On 4/27/2011 5:13 AM, shivangi nangia wrote:
> Dear gmx users,
>
> I need to design a starting configuration of a polypeptide with 
> charged side chains sitting in a box of water with Cl- ions within 7 
> ang of its radius.
>
> I realize that in such a system like charges will essentially prefer 
> to be as far as possible from each other, but I still need the above 
> stated configuration.
>
> Is there an easy way to specify the distance of the anions to be added 
> from the peptide ?

No. You will have to find water molecules a suitable distance from your 
solute and replace them by hand (and update your .top accordingly).

Mark