[gmx-users] Active site

[Justin A. Lemkul]

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That said, both of those tutorials are out of date, relying on very old Gromacs 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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 
========================================

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

========================================