From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Aug 11 2007 - 02:21:47 CDT

I am drawing a very large non-polymeric molecule in order to prepare a file for
molecular dynamics. The molecular mechanics program,though in OpenGl. does not
allow assigning unambiguously the R/S configuration at the various chiral
carbons (just because the program does not allow to magnify sections of the
molecule, which remain small on the screen). Also, the rendering of the MM is
not so clear cut as that of VMD.

When the pdb file is examined with VMD by magnifying sections, many R/S
mis-assignments come out. These would be difficult to correct with the MM
program because of what I said above.

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.

The MM program allows deleting atoms, and replacing them, graphically. I
imagine with VMD one should use terminal-window commands. What I can see (hot
key "0" pick mode mouse) are the atom name and its coordinates.

Thanks

francesco pietra

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