AMBER: bond connectivity among dummy atoms

From: Eric Hu <>
Date: Thu, 3 Mar 2005 10:56:32 -0800

Hi, I had a look at the trajectory from an amber 8.0 TI perturbation
(molecule --> nothing) with vmd. It seems that all atoms lost
connectivity with each other and only spheres are shown. Is this true?
My question is that if I perturb part of a molecule into a new
functional group will this new funcional group disconnects itself from
the core molecule?

It occurs to me that normally I have to manually add a bond between
two atoms in leap. Do I need to do so for all the dummy atoms too?

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Received on Thu Mar 03 2005 - 19:53:02 PST
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