Re: Overestimated PMF

From: Felipe Merino (
Date: Mon Jun 17 2013 - 10:15:07 CDT

Hi Giacomo,

Thanks for the reply. No, both domains separately have dG's around 20
something. The calculations are a bit expensive and that is why we did
not go further separating the other domain. In total it is like 400 ns
per domain so extending it is not particularly cheap.



On 06/17/2013 05:10 PM, Giacomo Fiorin wrote:
> Hello Felipe, are you summing the free energies from two separate
> calculations where you detach only one domain while keeping the other
> domain still bound?
> If you did that, this would explain why the discrepancy: those two
> terms are not necessarily additive.
> The correction would be to finish either simulation by also detaching
> the bound domain, and letting the entire protein go far enough from
> the DNA for all interactions to vanish.
> Giacomo
> On Mon, Jun 17, 2013 at 10:43 AM, Felipe Merino
> <
> <>> wrote:
> Dear all,
> I know this is a little bit off topic but i think somebody could
> help us here. We have been doing some umbrella sampling
> simulations to calculate the binding free energy of a protein-DNA
> complex. We are using the minimal interatomic distance as reaction
> coordinate. The thing is that the protein has two domains and we
> are only pulling them separately, so in the end we have always an
> endpoint with the other domain still bound (that was planned). In
> the end, the binding free energies are much higher than expected
> (around 25 kcal/mol). The point is that it sounds to me that there
> should be a correction on the PMF to account for the "confinement"
> of being bound to the other (still attached) domain (very much
> line in the case where you restrain the ligand when doing FEP
> annihilation) but i am not sure if this is correct. Any insights
> for this will be highly appreciated.
> Best
> Felipe

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