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
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