From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Dec 24 2015 - 08:45:43 CST
Hi Ardavan,
The easiest way is probably just to build the molecule you want as a pdb file, and scatter the desired number of copies as appropriate in your system prior to running psfgen.
Best,
Peter
> On Dec 24, 2015, at 8:37 AM, Ardavan Mehdizadeh <rdvnmzd_at_gmail.com> wrote:
>
> Hi,
> I was wondering if someone could help me with adding other ions and molecules in protein and water box system to a certain concentration; ions and molecule which are not available in VMD>Autoionize.
> Something like, Sodium Acetate or some molecules like Mannitol (Manna Sugar).
> Thanks.
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