[gmx-users] How to do Energy minimization and MD of protein-new ligand complex

[Justin A. Lemkul]

priyabrata panigrahi wrote:
> I am new to Gromacs. I have a protein where ligand  is bound to it. I 
> got this complex after carrying out docking of ligand to protein.The 
> ligand is new. So no topology and parameter files are available. At 
> first i want to carryout energy minimization of this complex and then I 
> want to find out how ligand interacts with the protein active site 
> residue by carrying a MD simulation. So can anyone guide me how to 
> proceed. It would be a great help
> 
> Thanks
> 

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

Of particular interest is the "GROMACS tutorial for drug - enzyme complex."  But 
before you proceed with collecting your own data following this procedure, 
please see here:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-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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