Re: Add ions/molecules different from Autoionize defaults

From: Peter Freddolino (
Date: Sun Dec 27 2015 - 22:04:00 CST

For the record, once youíve configured the antechamber interface, molefacture has a minimizer too. I havenít used Avogadro, so I canít compare the two, but wanted to clarify on the feature set.

> On Dec 27, 2015, at 7:25 AM, Josh Vermaas <> wrote:
> Hi Ardavan,
> Personally I'm a big fan of Avogadro for making small molecule pdbs. It has a minimizer built in! You'd need to change around the atom names so it matches what is in the topology file, but otherwise its perhaps the most intuitive interface for building molecules in a free editor.
> -Josh
> On 12/26/15 9:12 PM, Peter Freddolino wrote:
>> Well, you can build them in molefacture (a vmd plugin) or with any other molecule building software; that is probably the easiest.
>> Best,
>> Peter
>>> On Dec 25, 2015, at 1:28 PM, Ardavan Mehdizadeh <> wrote:
>>> Dear Peter,
>>> I really appreciate your help.
>>> How can I get those pdb files (e.g. Sodium Acetate pdb file), If you don't mind me asking?
>>> I should get them from available "data banks" or I should create them with software packages?
>>> Thank you so much,
>>> Ardavan.

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