Dear Seth
In my experience an "average" structure is frequently very unrepresentative
of any true molecular state, and the calculation process often gives rise to
bond lengths that differ mearkedly from their normal equilibrium values.
Within VMD a bond is determined by considering the euclidean distance
between 2 atoms, and if many atoms fall into this Euclidean range then many
bonds are formed and one essentially sees "spaghetti". This is a common
problem of using an "average" structure, I'd suggest that you instead find a
good representative structure, or the lowest, most visited structure.
I hope that helps
Hayden eastwood
Subject: AMBER: Average PDB - Unusual Bonds
Dear Amber Users,
I when I use ptraj to create an average stucture of several MD or annealing
runs with a NA structure, the structure has some unusual bond connectivity.
I can load the structure into leap and it looks fine, but in VMD and Rasmol
it looks the same. Has anyone else experienced such behavior?
Thanks,
Seth
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Received on Sun May 06 2007 - 06:07:30 PDT
