VMD-L Mailing List

From: Jay Shore (Jay.Shore_at_SDSTATE.EDU)
Date: Sun Oct 14 2007 - 22:42:42 CDT

Hi Amit,

You can use babel to convert between different structure file formats
(including mopac to pdb):
http://openbabel.sourceforge.net/wiki/Main_Page

Also, You can download structure files of small non-protein molecules from
the NCI database:
http://129.43.27.140/ncidb2/

I hope that this helps.
Jay

> 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.
>
>
>