mohsen ramezanpour wrote:
Dear Dr.Justin
I couldn't find any tutorial for doing free energy cycles with gromacs.
Then I was forced to select Umbrella sampling,I read your toturial and
it was very useful for me.I know it approximately good now.
Please let me know if there are any tutorial for free energy cycles.
I want to learn how I can do this.
When asking if there are tutorials, you should first check the Tutorials page;
that's why it exists:
http://www.gromacs.org/Documentation/Tutorials#Free_Energy_Calculations
That said, both of those tutorials are out of date, relying on very old Gromacs
versions. The fundamental principles still stand, though. Read in the manual
about new .mdp options and new methods for calculating free energy.
-Justin
Thanks in advance for your guidance
On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
mohsen ramezanpour wrote:
Dear All
I want to evaluate the binding free energy of protein-dryg.
My protein has so many atoms(5000 atoms),it make running too long.
I want to use Umbrella sampling for this.
Can I separate active site of protein (a radious of 3 nm around
of my drug )and do my work on this system?
I would think that such a fractured system would suffer from a
number of unpredictable artifacts. Protein structure is fairly
sensitive, so you'd have to apply lots of artificial restraints to
preserve geometry, but then what if even small conformational
changes are needed to for the protein to properly bind the drug?
Umbrella sampling is one of the more laborious ways of calculating
binding energies. Free energy cycles would probably be
significantly more efficient, since you can use a smaller box size
and (in all likelihood) run shorter simulations that still converge.
-Justin
Thanks in advance for your guidances.
Mohsen
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
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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