Hi Jason,
thanks for your quick reply.
>
> You had me panicked here a little bit (I had thought that the values below
> belonged to the total energy decomposition table).
Sorry for the inconvenience!
The results you get
> below are completely reasonable (and expected) for sidechain/backbone
> pairwise energy decomposition. The reason is the way the energies are
> decomposed in this case (sidechain/backbone). These potential terms are the
> result of the sum of the interactions of the sidechain (or backbone) atoms
> of Resid 1 with ALL of the atoms of Resid 2. Thus, the sidechain pairwise
> interaction Residue A -> Residue B will be defined differently than the
> pairwise interaction Residue B -> Residue A, so there's no reason to expect
> them to be the same.
>
> This way of decomposing allows you to simply calculate the total as the sum
> of the sidechain and backbone contributions (which is what is done in the
> code). THESE values (the Total tables), should represent all-to-all in
> terms of atomic pairwise potential terms between the two residues, so I
> believe the values in those tables should match almost (if not) exactly. Do
> they?
>
They do, here's the corresponding lines:
Resid 1 | Resid 2 | Internal | van der Waals |
Electrostatic | Polar Solvation | Non-Polar Solv. |
TOTAL
ASN 33 | ARG 41 | 0.000 +/- 0.000 | -1.200 +/- 0.317 | -4.847
+/- 3.207 | 3.902 +/- 2.685 | -0.318 +/- 0.033 | -2.462 +/- 4.195
ARG 41 | ASN 33 | 0.000 +/- 0.000 | -1.200 +/- 0.317 | -4.847
+/- 3.207 | 3.902 +/- 2.685 | -0.316 +/- 0.033 | -2.460 +/- 4.195
Seem to only have slight differences in the Non-Polar Solvation part. A
quick look at some other residue pairs seems to confirm this.
Thaks again!
Best, Chris
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Received on Mon Apr 04 2011 - 08:00:03 PDT
