[gmx-users] md simulation for ternary complex

[Justin A. Lemkul]

kala wrote:
> Dear All,
> 
> I am planning to perform a simulation of a protein ternary complex with 
> 2 ligands and Zn molecule. The protein has 2 chains with 430aa.Is it 
> possible to do simulation for the protein complex. I have got sufficient 
> hardware configuration for the dynamics study. As am new to perform such 
> complex simulations kindly help me to start with.
> 

You can certainly simulate such a complex, but it may not be very easy.  You 
should start with basic tutorial material, including the tutorial about a 
drug-enzyme complex to get yourself familiarized with proper topology organization.

http://www.gromacs.org/Documentation/Tutorials#General

Then, you should prepare yourself for the potentially arduous task of proper 
ligand parameterization.  This is an advanced topic, so be prepared to invest a 
significant amount of time in getting ligand parameters right.  This may be a 
matter of weeks or months, if done properly.  PRODRG is not sufficient for 
generating reliable parameters, though this is not stated in the drug-enzyme 
tutorial.

http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

The other complication is the Zn ion.  Proper treatment of transition metals is 
not trivial, and if this residue plays some important role in the function of 
the protein, a standard MM treatment may not be appropriate.  See the above 
Parameterization page, particularly the Exotic Species section.

-Justin


> kala bharath
> 

-- 
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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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