jorge_quint...@ciencias.uis.edu.co wrote:
Dear all.
A few days ago I posted a question related with binding energy between two
proteins using the LIE method, in that case my energies were between -2400
to -2700 kcal/mol. Later, I tried to obtain the same information doing
several simulations employing the FEP method in combination with ffamber94
force field, only I used one of the complex model obtained with a docking
tool (protein-protein). with the FEP method my energy is completely
different compared to the LIE method.
result with LIE: -2600 kcal/mol
result with FEP: 7400 kcal/mol
What happen with these result. I guess these results might be slightly
the same. isn't it?. I'll appreciate your support.
I don't know how reliable decoupling an entire protein will be (nor do you give
any details about your protocol, precluding any assessment of its reliability),
but there may be significant error bars. Another technique that you might
consider is the calculation of PMF using the pull code.
-Justin
--
========================================
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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