Re: Add ions/molecules different from Autoionize defaults

From: Tristan Croll (
Date: Tue Dec 29 2015 - 07:12:10 CST

If it's a fairly common small molecule like acetate ion then Hic-UP is a very useful site for getting heavy atom coordinates. You'll likely have to do a lot of renaming (both residue and atom names) - CHARMM nomenclature diverges a lot from the PDB for non-protein/non-nucleic residues.

Tristan Croll
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
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> On 27 Dec 2015, at 1:38 PM, 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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