Re: [AMBER] protein+DNA simulation

From: Thomas Cheatham III <>
Date: Wed, 22 Aug 2012 16:17:41 -0600 (Mountain Daylight Time)

> i am trying md simulation for dna+protein system ...but i don't want
> to take combined crystallographic structure from pdb bank.

I suggest using any experimental information you can find, and ideally the
correct crystal structure.

> My problem is that if i take separate structure of protein and and
> separate DNA structure from pdb bank and merge it in common pdb file
> ...then how i will ensure that after minimization and long md run,
> protein will go and attach to DNA with lowest free energy ...because
> it can get trap to any random position with not the lowest possible
> structure.

Correct. There is no guarantee that even a reasonably long (say
microsecond scale) simulation will be able to "correctly" dock the
DNA/protein or that long MD will find the "best" protein-DNA complex

> Moreover, placing protein close to DNA and then after MD checking free
> energy is not feasible , as i need to search for as many orientation
> of protein near DNA for best feasible protein-DNA structure.


> I was thinking of doing it with ROSETTA , but is there any better
> option in AMBER or any software.

There is no automagic way that I know of using molecular dynamics to
correctly dock the DNA. Either investigate a docking program (and even
this will be of questionable accuracy) or find a correct/reasonable
experimental structure. Even with the DE Shaw Anton machine, accurately
probing protein-ligand interaction is hard, let alone investigating
DNA-protein interaction with commodity hardware. I also recommend
searching the literature on protein-DNA interaction with simulation as
there may be alternative means to address your scientific questions...


AMBER mailing list
Received on Wed Aug 22 2012 - 15:30:02 PDT
Custom Search