On Jul 3, 2014, at 12:41 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
> Dear amber users,
>
> I have a system which contains a protein subunit but using PBC, I'm
> effectively simulating a thread of infinite length of this subunit.
> However, I want to use the MM/PBSA to calculate the energy of interaction
> between the system and one of its adjacent PBC image. Is that possible?
Maybe. You'll have to create a new topology with your original protein subunit and the one extra periodic image whose energy you want to calculate. Then you need to process your trajectory and create a _new_ set of coordinates with just the 2 images of the protein subunit you want to analyze (and nothing else -- it needs to match your new prmtop file). Then you can use MM/PBSA or MM/GBSA to analyze the energies -- you would basically analyze the energies of an isolated subunit and subtract double that number from the energy of the larger system with the 2 periodic images.
There are no tools that can automate any of those tasks (except MMPBSA.py for the last part). It would be _much_ easier to compute the interaction energy without an implicit solvent model between a single subunit and all of its periodic images. But these are fundamentally different calculations, since the former includes the effects of solvent screening of the electrostatic interactions whereas the latter would not. It all depends on what exactly you want to compute.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 03 2014 - 13:30:02 PDT
