AMBER Archive (2008)

Subject: AMBER: Energy minimization of protein-ligand complex

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Tue Jul 29 2008 - 02:18:57 CDT

Hi everyone,

I have a protein-ligand docked complex and I'm trying to apply energy
minimization to take care of the steric clashes and hopefully optimize
ligand position and geometry. Currently I'm running the minimization
in gas phase and the input looks like:

 &cntrl
  ntxo = 1,
  ntf = 1, ntb = 0,
  dielc = 4,
  cut = 12.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,
  imin = 1, maxcyc = 1500,
  ncyc = 500, drms = 0.0001
  ibelly = 1, bellymask=':ligname | (:ligname < :12.0)'
 &end
 &ewald
  eedmeth= 5,
 &end

My question is if it's better off to use the GB model (for example
igb=1) than gas phase for that purpose?

I also want to run MM-GBSA (w/ igb=1) on this complex, so would GB
minimization offer better consistency and results if the same
parameters (dielc, intdiel, extdiel, saltcon etc.) are used?

Could anyone kindly give me an example GB minimization input with
restraint that can be used to substitute the above?

Thanks a lot in advance,

-DX
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