[gmx-users] Reg: MDS of docked comples

[Rohit Farmer]

Hi there ... i am new to GROMACS ... however i am able to do mds of
simple protein structures under default configurations ... now i want
to simulate docked complexes .. the docking is done using autodock
.... in order to see the hydrogen bond variations between the ligand
and the active site lining residues.... but for this i don't have any
protocol ... therefore if anyone can suggest me a standard protocol
for simulating docked compexes along with the mdp files ... then
please do suggest ...


Regards

Rohit

-- 
Rohit Farmer
M.Tech Bioinformatics
Department of Computational Biology and Bioinformatics
Jacob School of Biengineering and Biotechnology
Sam Higginbottom Institute of Agriculture, Technology and Sciences
(Formerly known as Allahabad Agricultural Institute - Deemed University)
Allahabad, UP, INDIA - 211 007
Ph. No. 9839845093, 9415261403
e-Mail rohit.farmer at gmail.com
Blog http://rohitsspace.blogspot.com