Re: vmd-l: Small molecules

From: Christopher Harrison (
Date: Fri Oct 12 2007 - 23:41:23 CDT

Hi Amit,

I may be mistaken but i believe Molden, which is freely available,
can read mopac files. You could then save as a pdb and load it into

Perhaps if you brought this issue to Jan Saam's attention, the author
of the vmd molefacture plugin to build and model small molecules, he
might consider adding the ability to read mopac files since the
format is fairly standard and it is a widely used program in the
computational community.


On Oct 12, 2007, at 6:02 PM, Amit wrote:

> Hi,
> I'm looking for a way to work with small non-protein molecules like
> the hormone epinephrine or the drug acetaminophen, on VMD. I have a
> chemistry software that allows me to build such molecules from
> scratch and save them, but the format of the saved file is mopac
> (.mop), which VMD doesn't seem to recognize. Is there a free tool I
> can use to convert these files to something VMD can work with?
> Alternatively, is there a way of generating such small molecules
> with VMD?
> Cheers,
> Amit.
> Peek-a-boo FREE Tricks & Treats for You! Get 'em!

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