From owner-chemistry -x- at -x- ccl.net Mon Mar 5 18:32:00 2007 From: "=?ISO-8859-1?Q?Tom=E1s_Pe=F1a_Ruiz?= truiz++ujaen.es" To: CCL Subject: CCL: Concerning NBO bond orders Message-Id: <-33735-070301110610-24044-z7sW5S1I8EsmP06e4T61SQ|a|server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Tom=E1s_Pe=F1a_Ruiz?= Content-Type: multipart/alternative; boundary="------------060707080203000104070305" Date: Thu, 01 Mar 2007 16:09:06 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Tom=E1s_Pe=F1a_Ruiz?= [truiz(_)ujaen.es] This is a multi-part message in MIME format. --------------060707080203000104070305 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hallo!! I'm studying a chemical reaction and trying to compare the modification of the bond orders among reactants, molecular complex and transition state. NBO provides a series of bond orders calculated under different assumptions. Which kind of bond orders could be more appropiate, Wiberg's indexes, atom-atom overlap NAO bond order, NLMO bond orders? Thanks Tomás Konrad Hinsen hinsen!^!cnrs-orleans.fr wrote: >Sent to CCL by: "Konrad Hinsen" [hinsen]~[cnrs-orleans.fr] >On 28.02.2007, at 07:07, Pradipta Bandyopadhyay pradipta:iitg.ernet.in wrote: > > > >>Applying GNM to a protein (whose structure is a bit open), I found that in >>some regions B-factors obtained from calculation is different from >>experimental one (for the rest other regions these are close). This >>probably means using one gamma may not be enough. Does anyone know if >>there is any simple way to use more than one gamma in GNM (any other >>suggestion would be appreciated also)? >> >> > >It is certainly possible to use different gammas for the different interacting pairs, but I am not >aware of anyone having done so in a GNM. > >If you are reasonably sure that the experimental B factors are reliable, then my first suggestion >would be to try an elastic network model, i.e. a model taking into account the directions of atomic >displacements. This increases the number of coordinates in your system by a factor of three, but >that difference matters only for huge proteins. You gain in two points: > > 1) The description with three coordinates per C-alpha atom is in itself more precise and thus >more realistic. > > 2) The GNM potential is physically unrealistic in not being invariant under rotations. This >means that it penalizes global rotations (which you probably don't care about), but also rotational >domain motions which you may well have in your protein. > >There is also a wider choice of potential models that have been published for elastic network >models. The most widely used variety of elastic network models uses a force constant that depends >on the interatomic distance in the input configuration, nearby atom pairs interacting stronger than >more distant ones. In this family we find, in historical order: > > 1) A exp(-r^2) decrease with distance: > K Hinsen > Analysis of domain motions by approximate normal mode calculations > Proteins 33:417-429 (1998) > http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_1998 > > 2) A more complex function obtained from fitting to the Amber94 all-atom potential: > K Hinsen, A J Petrescu, S Dellerue, M C Bellissent-Funel, and G R Kneller > Harmonicity in slow protein dynamics > Chem. Phys. 261(1+2):25-37 (2000) > http://dirac.cnrs-orleans.fr/plone/publications/all-publications/Hinsen2000a > > 3) A step function: constant up to a cutoff distance, then zero (like for GNM): > A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar > Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model > Biophys. J. 80, 505515 (2001) > >The best model is probably the one described in 2). You can find a ready-to-use implementation in >the Molecular Modelling Toolkit (http://dirac.cnrs-orleans.fr/MMTK, it's called CalphaForceField >there). There is also a Web server that performs various normal-mode based calculations (including >B factors) using this model for any PDB file you submit; the address is > > http://www.bioinfo.no/tools/normalmodes > >I remember having seen a paper that modifies the elastic network model in choosing the force >constants in a more protein-specific way, but I don't have the reference at hand. > >Konrad. >-- >--------------------------------------------------------------------- >Konrad Hinsen >Centre de Biophysique Molculaire, CNRS Orlans >Synchrotron Soleil - Division Expriences >Saint Aubin - BP 48 >91192 Gif sur Yvette Cedex, France >Tel. +33-1 69 35 97 15 >E-Mail: hinsen||cnrs-orleans.fr >---------------------------------------------------------------------> > > > > > > --------------060707080203000104070305 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hallo!!

I'm studying a chemical reaction and trying to compare the modification of the bond orders among reactants, molecular complex and transition  state. NBO provides a series of bond orders calculated under different assumptions. Which kind of bond orders could be more appropiate, Wiberg's indexes, atom-atom overlap NAO bond order, NLMO bond orders?

Thanks

Tomás

Konrad Hinsen hinsen!^!cnrs-orleans.fr wrote:
Sent to CCL by: "Konrad  Hinsen" [hinsen]~[cnrs-orleans.fr]
On 28.02.2007, at 07:07, Pradipta Bandyopadhyay pradipta:iitg.ernet.in wrote:

  
Applying GNM to a protein (whose structure is a bit open), I found that in
some regions B-factors obtained from calculation is different from
experimental one (for the rest other regions these are close). This
probably means using one gamma may not be enough. Does anyone know if
there is any simple way to use more than one gamma in GNM (any other
suggestion would be appreciated also)?
    

It is certainly possible to use different gammas for the different interacting pairs, but I am not 
aware of anyone having done so in a GNM.

If you are reasonably sure that the experimental B factors are reliable, then my first suggestion 
would be to try an elastic network model, i.e. a model taking into account the directions of atomic 
displacements. This increases the number of coordinates in your system by a factor of three, but 
that difference matters only for huge proteins. You gain in two points:

	1) The description with three coordinates per C-alpha atom is in itself more precise and thus 
more realistic.

	2) The GNM potential is physically unrealistic in not being invariant under rotations. This 
means that it penalizes global rotations (which you probably don't care about), but also rotational 
domain motions which you may well have in your protein.

There is also a wider choice of potential models that have been published for elastic network 
models. The most widely used variety of elastic network models uses a force constant that depends 
on the interatomic distance in the input configuration, nearby atom pairs interacting stronger than 
more distant ones. In this family we find, in historical order:

	1) A exp(-r^2) decrease with distance:
		K Hinsen
		Analysis of domain motions by approximate normal mode calculations
		Proteins 33:417-429 (1998)
		http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_1998

	2) A more complex function obtained from fitting to the Amber94 all-atom potential:
		K Hinsen, A J Petrescu, S Dellerue, M C Bellissent-Funel, and G R Kneller
		Harmonicity in slow protein dynamics
		Chem. Phys. 261(1+2):25-37 (2000)
		http://dirac.cnrs-orleans.fr/plone/publications/all-publications/Hinsen2000a

	3) A step function: constant up to a cutoff distance, then zero (like for GNM):
		A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar
		Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model
		Biophys. J. 80, 505515 (2001)

The best model is probably the one described in 2). You can find a ready-to-use implementation in 
the Molecular Modelling Toolkit (http://dirac.cnrs-orleans.fr/MMTK, it's called CalphaForceField 
there). There is also a Web server that performs various normal-mode based calculations (including 
B factors) using this model for any PDB file you submit; the address is

	http://www.bioinfo.no/tools/normalmodes

I remember having seen a paper that modifies the elastic network model in choosing the force 
constants in a more protein-specific way, but I don't have the reference at hand.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Molculaire, CNRS Orlans
Synchrotron Soleil - Division Expriences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen||cnrs-orleans.fr
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