leila karami wrote:
Hi
I want to compare DNA-binding affinity of PRH protein by mutation of
some aminoacids.
I think KD (dissociation constant) is related to binding affinity.
I dont know how do I obtain KD (dissociation constant) by MD simulation
and gromacs (what command).
There isn't any one, single command that will do this for you.
If there is another way, please guide me.
What you are asking to do is potentially very difficult. To obtain Kd, you
would need to calculate the binding free energy of your complex, which would
require a thermodynamic cycle. Unfortunately, given the very highly-charged
nature of DNA, the results may or may not be reliable. Decoupling a species
with a net charge leads to very large error bars, from what I've read.
You could potentially use the free energy code to do the "mutations" and obtain
values of delta(deltaG) relative to the WT, but that assumes you can actually
accomplish what I outlined in the above paragraph.
You can try g_lie, which gives an estimate of the free energy, but I don't know
how reliable it is, having never used it, especially for a large and complex
"ligand" such as DNA.
-Justin
Any help will highly appreciated!
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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