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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 27 03:01:38 CEST 2011

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).


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