On Thu, Jan 21, 2016 at 1:56 PM, Kucharski Jr., Amir N <
amir.kucharski.uky.edu> wrote:
> Hi,
>
> I am trying to use MMPBSA to calculate the free energy of an unbound
> protein (that is, there are no ligand or complex files to be used, only a
> receptor file). Is there any way of doing this? Any help is much
> appreciated.
>
Only free energy differences have any real meaning. So when you say you
want a "free energy of an unbound protein", that is an undefined problem.
To get a free energy difference, you need at least two states. In typical
MM/PBSA applications, these two states are bound and unbound.
Single-species (i.e., only dealing with an "apo" receptor, for instance)
MM/PBSA-like calculations are often called stability calculations because
they compare the relative stability of two conformations, or two clusters.
This is still a free energy difference. Or maybe you want free energies of
solvation, where the difference is between gas phase and solution. So you
really need to be a lot more specific about what *exactly* you want to
calculate. And then I suggest looking at the manual, which has information
about doing stability calculations (if that is, in fact, what you want to
do).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 21 2016 - 12:00:03 PST
