Re: CCL:MD after Autodock



Hi Sandro,
 I'm not really sure what you are trying to do....Did you perform the geometry
 optimization and minimization to both the ligand and the receptor?  In addition,
 do you
 mean that you optimized (via ab initio) then minimized (using MM)?  If you are
 trying
 to find the best docking pose of a ligand to a given receptor here is what I
 would do:
 1. Optimize the active site of the receptor (if you don't have a crystal
 structure) and
 the ligand  i.e. ab initio geometry optimization.  If you do this at the
 HF/6-31G*
 level then you can generate a RESP charge set which is excellent for docking.
 2.  Do the docking in Autodock.
 3.  Rescore the poses.  The scoring function in Autodock is not necessarily the
 best.
 It was trained on a limited number of molecules and used OPLS charges.  You can
 however
 rescore the poses using a MM program that will allow you to calculate VdW,
 electrostatic, potential energy (of ligand), etc...and use this to rank the
 poses.
 As far as a MD simulation.....you could do one if you wanted to observe the
 interaction
 between the ligand and the receptor.  This might be useful to determine if the
 ligand
 is equilibrated (i.e. prefers one geometry) in the active site and the rate at
 which it
 goes into and out of the active site.  Hope this helps.
 Cheers,
 Joey
 ----------------------------------
 Joey Harriman
 MSc Computational Chemistry
 University of New Brunswick
 Room 228
 Toole Hall
 s808o.-at-.unb.ca
 476-6543
 ----------------------------------
 Quoting sa.cosco.-at-.virgilio.it:
 > Dear CCL
 > I performed a partial flexible docking analysis of some ligands, using
 Autodock,
 > on a receptor modelled by means of homology building .The complexes
 obtained
 > were geometrically optimized and energetically minimized. Is it really
 necessary
 > to perform a MD simulation after the docking and the minimization? Any
 suggestion
 > will be appreciated
 > Best regards
 > Sandro
 >
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