Re: Add ions/molecules different from Autoionize defaults

From: Peter Freddolino (
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.

> On Dec 24, 2015, at 8:37 AM, Ardavan Mehdizadeh <> 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.

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:22:21 CST