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