On 19/11/2011 6:42 AM, Ben Reynwar wrote:
On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 18/11/2011 8:10 AM, Ben Reynwar wrote:
Dear gromacs list,
Does anyone know how well current force fields capture the energetics
of non-specific protein-protein interactions? I'm simulating a
protein with an arm that alternates between (apparently) non-specific
adsorption to the main-body of the protein and free movement in the
solvent. Can I place any trust in the results of an MD simulation for
something like this? I haven't seen any comparison of experimental
results with simulation results of the energetics of non-specific
protein-protein interactions so I'm a little skeptical about it.
Currently I'm using generalized born implicit solvent, which is
perhaps a mistake when solvation energies could be critical to the
results.
I'd be very skeptical unless you can observe many adsorption/desorption
processes and with explicit solvent (though they're probably mutually
exclusive).
Mark
I think I asked my question poorly.
In a perfect simulation with explicit solvent and infinite sampling,
roughly what kind of error might one expect for peptide-peptide
interaction energies due to the force field?
Presumably there are papers out there that go into this, but I'm not
finding them. If anyone knows of any directions to point me in, I'd
really appreciate it.
I don't recall having ever seen an explicit solvation simulation on even
a small peptide that claimed exhaustive sampling, never mind a system
that shows such complex behaviour. It's possible someone has used
slow-growth methods to grow a small peptide ligand onto the side of a
protein, and that could give a guide to the accuracy of inter-protein
energetics, but I've never gone looking for such.
Mark
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