From: J. Rui Rodrigues (
Date: Thu Sep 24 2009 - 07:22:09 CDT


Your .mol2 contains only single bonds. If you want to see double bonds, you could edit
the @<TRIPOS>BOND section. The bond order is the fourth column in that section. For more
on mol2 format, google for Tripos mol2 format.

Hope this helps,
Rui Rodrigues

On Wed, 23 Sep 2009 13:22:27 -0400, Taufik Al-Sarraj wrote
> Hello,
> I have a small molecule that i would like to visualize using VMD, the
> molecule is in mol2 format. if i view the molecule the double bond is
> shown as a single bond. How can i correct this?
> In AMBER i can load the *.lib file but i cannot load the *.lib file into
> VMD.
> Best,
> Taufik

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