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

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 21 14:19:24 CEST 2010

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


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:




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


More information about the gromacs.org_gmx-users mailing list