Thanks to all of you for your helpful suggestions!
We are using sander and then convert the data using ptraj.
The average distance between C6 and the hydrogens is around 9 angstroms. If they are bonding to another atom, sometimes this new bond has normal length, while it is up to 8 angstroms in other cases. However, the outcome is very different for the respective ensemble members.
Today we calculated another analog (differing only in one side chain), and in this case the rupture occurs in only 60% of the output .pdb, not 100%.
But since it seems to be OK just to change the denotation in the output .pdb I think we will do this. I will also check the structures with another viewer as suggested.
Thanks again!
Sebastian Enck
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Received on Wed Feb 15 2012 - 16:00:02 PST
