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From: Jason Swails <jason.swails.gmail.com>

Date: Mon, 4 Apr 2011 07:24:51 -0700

Hello,

On Mon, Apr 4, 2011 at 7:11 AM, Christoph Malisi <

christoph.malisi.tuebingen.mpg.de> wrote:

*>
*

*> In all tables in FINAL_DECOMP_MMPBSA.dat, there are two energies for
*

*> each residue pair, e.g.
*

*>
*

*> ASN 33 | ARG 41 ...
*

*>
*

*> and
*

*>
*

*> ARG 41 | ASN 33 ...
*

*>
*

*> The values in these lines from the same table (e.g. complex, total
*

*> energy decomposition) are more or less similar, but not always exactly
*

*> the same, e.g. from complex sidechain energy decomposition:
*

*>
*

You had me panicked here a little bit (I had thought that the values below

belonged to the total energy decomposition table). 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?

Hope this helps,

Jason

Resid 1 | Resid 2 | Internal | van der Waals |

*> Electrostatic | Polar Solvation | Non-Polar Solv. |
*

*> TOTAL
*

*>
*

*> ASN 33 | ARG 41 | 0.000 +/- 0.000 | -0.656 +/- 0.173 | -2.312
*

*> +/- 3.191 | 1.950 +/- 2.682 | -0.151 +/- 0.040 | -1.169 +/-
*

*> 4.172
*

*>
*

*> ARG 41 | ASN 33 | 0.000 +/- 0.000 | -1.183 +/- 0.315 | -4.760
*

*> +/- 3.185 | 3.822 +/- 2.655 | -0.316 +/- 0.033 | -2.437 +/-
*

*> 4.159
*

*>
*

*>
*

*> My question is if these two values are supposed to be the same/similar
*

*> energies, and the difference stems form uncertainties/variance in the
*

*> calulation, or if the total pairwise energy is the sum of these two, and
*

*> how they are split.
*

*>
*

*> Thanks,
*

*> Chris
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Mon, 4 Apr 2011 07:24:51 -0700

Hello,

On Mon, Apr 4, 2011 at 7:11 AM, Christoph Malisi <

christoph.malisi.tuebingen.mpg.de> wrote:

You had me panicked here a little bit (I had thought that the values below

belonged to the total energy decomposition table). 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?

Hope this helps,

Jason

Resid 1 | Resid 2 | Internal | van der Waals |

-- 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/amberReceived on Mon Apr 04 2011 - 07:30:08 PDT

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