[gmx-users] md simulation for ternary complex

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 5 16:53:15 CET 2011

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.


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 


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.


> kala bharath


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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