VMD-L Mailing List

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Tue Apr 13 2004 - 09:01:56 CDT

hi vmd'ers,

i'm trying to visualize zeolite structure with some of the silicon atoms
replaced by aluminiums. the problem is, that vmd doesn't always connect
aluminium to all 4 neighbouring oxygens (sometimes it doesn't connect it
at all).

i can see many error messages "MolAtom xy: Exceeded maximum number of
bonds (8)" in the vmd console window - is this somehow related?

the problem also could be that i have "core" and "shell" representations
of oxygen atoms that lay very close to each other...

another question - when i have sequence of xyz files - is vmd
recalculatind bond structure for every step or is it using its first
guess for all frames? if it is the latter case - is there any way how to
change this behaviour?

i can send you the structure if it would help you, just let me know if
you need it.

thanks for your help, 

-- 
Lubos
_@_"