From: Jean-Patrick Francoia (
Date: Tue Apr 29 2014 - 09:01:39 CDT

Le 29/04/2014 15:54, Axel Kohlmeyer a écrit :
> On Tue, Apr 29, 2014 at 8:49 AM, Jean-Patrick Francoia
> <> wrote:
>> Hello,
>> I wonder if there is a way to visualize a SMILES string in VMD, and possibly
>> in 3D. I did a bit of digging but found nothing clear.
>> How do you do that ?
> find a program/tool that converts a SMILES string into a supported
> file format and then load that file into VMD.
>> Regards
>> JP

I forgot to mention that:

Yes I know a bunch of softwares like Avogadro to visualize/export a
SMILES string, but most of them can't handle my number of amino acids
(>15000). That's another specification. I know VMD is pretty fast
compared to Avogadra for example, when it comes to open a file.