On Mon, Jan 7, 2013 at 3:50 PM, Norah Schlacter
<norah.schlacter.gmail.com>wrote:
> Dear all,
>
> I recently updated my amber with the new bugfix. However during system
> set up, tleap started to give me a different distribution of counter
> ions afterwards.
>
> Before that tleap used to locate the ions away from the protein (7-11A
> in a 13A water box) now it is putting all the Cl-'s close to (5-7A) to
> Arginines and Lysines.
>
>
> I was wondering what part of the update is responsible for that kind of
> change. I checked the summary of the bugfix, couldn't figure out what
> part of the update affects tleap.
>
There are no parts of any AmberTools 12 bugfix that affect the tleap source
code, so I'm not sure how to explain what you're seeing based on the
available information...
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jan 07 2013 - 13:30:02 PST
