VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Aug 11 2007 - 08:43:09 CDT

Hi Francesco,

Francesco Pietra wrote:
> Is any provision with VMD to epimerize chiral centers, i.e., step by step
> inverting the configuration at various centers? Clearly this would involve -
> for example - exchanging the position of two atoms (or two groups of atoms) at
> a chiral center. For example exchanging the position of atom H with group OH at
> a chiral carbon atom. Or inverting the configuration at a H-bearing carbon at
> the fusion point of two rings.
>
if you grab a CVS snapshot of vmd, you can find a proc for inverting
chirality (::Molefacture::invert_chir) in molefacture_geometry.tcl (in
the molefacture directory of the plugin source. You can either make use
of this proc in writing your own script, or use molefacture (which now
includes an "invert chirality" button) to edit your molecule directly.
Please let me know if you have any problems.

Best,
Peter