9 Angstroms? Do you by chance mean 0.9? Do you mind sending me the
initial topology and restart (.top and .crd) files from the web site?
You can send off list or on list, as you prefer.
On Wed, Feb 15, 2012 at 6:37 PM, Sebastian Enck <encks.scripps.edu> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Feb 15 2012 - 19:00:02 PST
