I see.
The intention was more to compare entropic stabilities between different
topologies. As a simple example, if you took the tripeptide Gly-Ala-Phe,
or would it compare to the inverted sequence of Phe-Ala-Gly? Since both
have the same atoms, the comparison ought to be meaningful. There are
other things one could do along the same lines.
So there isn't a particular reason that ptraj can't do this, it's just the
input file MM-PBSA generates? That is to say, I could calculate the
entropic term with ptraj without that mask and it would represent an S
(entropy) term, and I'd derive my own delta-S? The ptraj calculation
completed when I removed the mask, and the output had numbers for entropy,
although I've no sense of how meaningful they were.
Alternatively, if I did have a receptor and ligand defined, would I get not
only the delta-S, but also the absolute S for the complex and for each of
the receptor and ligand? Because if that is the case I could just
arbitrarily define half the molecule to be the receptor and the other half
the ligand, no?
I had thought about just trying the normal mode method, but it seemed as
though it would be a) much slower, since energy minimization is required
(maybe I'm confused about that), and b) gives poorer results for more
complicated systems (or at least my impression was that the quasi-harmonic
approach was now in favour).
Thanks for clarifying what the error was. If you've any opinions on my
above options, please let me know :)
~Aron
On Tue, Nov 13, 2012 at 5:55 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Nov 13 2012 - 16:00:03 PST
