On Mon, Feb 27, 2012 at 2:17 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
> I did a protein-drug complex MD study. I calculated the MM/GBSA
> per-residue analysis. I found the drug has a per-residue energy too, what
> is the physical meaning of this number? Should we interpret it as the
> internal binding energy of the drug at gain or loss upon binding with the
> protein? My gut feeling is when we are talking about per-residue energy, I
> should only got the energy for protein residues, I am not quite sure why
> the drug have energy contribution to it too. Please kindly instruct.
>
I'm not sure what you mean by "I found the drug has a per-residue energy
too". I'm going to assume you mean that the ligand has a non-zero
per-residue energy completely by itself (that is, if you run a per-residue
decomposition on a single residue, the ligand, you get non-zero results).
If this is the case, then that number is an "internal energy" of sorts. I
think, at its most basic, the per-residue decomposition is simply summing
up the values of every energy term in which at least one of the involved
atoms resides in your residue. Therefore, if you have two atoms in a
residue that are not connected by bonds, angles, or dihedrals, they will
experience non-bonded interactions with each other. Since at least one
atom is present in the residue (that is, both atoms are), this contribution
is added to that residue's decomposed energy contribution. Therefore, I
would expect it to be non-zero.
These internal energies will cancel out when taking a difference, so the
DELTA is the section that you should be looking at for that kind of
information.
I also did a MM/GBSA total binding energy for the same complex, why it is
> different from the sum of MM/GBSA per-residues' total energy?
>
It is different because of double-counting. Say atom 1 is in residue 1 and
atom 10 is in residue 2. The non-bonded interactions between atoms 1 and
10 are added to both residue 1 and residue 2, even though it's only
included in the total energy once.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 27 2012 - 08:30:02 PST
