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From: Balazs Jojart <jojartb.gmail.com>

Date: Fri, 24 Jun 2011 23:47:03 +0200

Hello,

Ok, thanks for everybody for the explanation(s).

If I have two trajectories with and without ligand, then:

1) average structure calculation for the whole protein

2) quasi harmonic analysis for the ith residues at the binding site in

the first and in the second trajectory

3) then comparing the obtained values we can make estimations about the

rotameric states in the two trajectories (as dr Cheathem wrote:

particular rotameric states locked out comparing free vs. bound)

In the above mentioned way I was thinking about the decomposition,

because in the nmode analysis such a calculation is not possible

(consider only one residue), if I remember correctly. Maybe not ...

Balazs

On 06/24/2011 11:14 PM, Thomas Cheatham III wrote:

*>> If we use quasi-harmonic approximations instead of normal mode analysis,
*

*>> then the decomposition is possible. Or not?
*

*> You *can* calculate from normal modes or quasi-harmonic the vibrational
*

*> entropy for each isolated amino acid, however this will not tell you much
*

*> since (a) this result is not very sensitive to changes in the amino acid
*

*> structure, (b) it neglects the coupling of the surroundings. You can try
*

*> this to verify to yourself...
*

*>
*

*> As Professor Case mentioned, the dominant entropic factors are from the
*

*> low-frequency modes which represent large-scale collective motions among
*

*> many atoms, for example bending or opening. At the opposite extreme are
*

*> the high frequency motions (bonds) which are only between two atoms--
*

*> these are relatively independent of the environment and contribute very
*

*> little (or effectively a constant amount) to the entropy.
*

*>
*

*> 90% of the motion (and therefore the conformational entropy around a given
*

*> substate/minima) is in the first ~10% of the modes. By decoupling to the
*

*> residue level, you effectively loose this.
*

*>
*

*> If I were to think about decoupling, I would look at means to estimate
*

*> configurational entropy (changes) of the molecules rather than
*

*> vibrational; i.e. are particular rotameric states locked out comparing
*

*> free vs. bound? Is there greater freedom of movement in one simulation
*

*> compared to another? Estimating configurational entropy differences is
*

*> more tricky; I would look for work by MK Gilson and co-workers.
*

*>
*

*> --tec3
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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Received on Fri Jun 24 2011 - 15:00:04 PDT

Date: Fri, 24 Jun 2011 23:47:03 +0200

Hello,

Ok, thanks for everybody for the explanation(s).

If I have two trajectories with and without ligand, then:

1) average structure calculation for the whole protein

2) quasi harmonic analysis for the ith residues at the binding site in

the first and in the second trajectory

3) then comparing the obtained values we can make estimations about the

rotameric states in the two trajectories (as dr Cheathem wrote:

particular rotameric states locked out comparing free vs. bound)

In the above mentioned way I was thinking about the decomposition,

because in the nmode analysis such a calculation is not possible

(consider only one residue), if I remember correctly. Maybe not ...

Balazs

On 06/24/2011 11:14 PM, Thomas Cheatham III wrote:

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Received on Fri Jun 24 2011 - 15:00:04 PDT

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