On Tue, Nov 13, 2012 at 4:52 PM, Aron Broom <broomsday.gmail.com> wrote:
>
> Has anyone else successfully run the entropy calculations with ambertools12
> fully updated? One potential issue is that I don't really have receptors
> and ligands, it's just a single trajectory of a single peptide that is
> being considered a complex, but the non-entropy run completed without
> trouble there, so I'm not sure that is the issue.
>
This is indeed the issue. The quasi-harmonic calculation (which is what
you get via "entropy=0") does not support calculations without a ligand and
receptor. Nobody has tried this before (or they didn't report it),
although I'm not sure what this tells you about the system in the context
of a so-called 'stability' calculation.
Normal mode analysis should still work without a receptor/ligand.
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 13 2012 - 15:00:02 PST
