I may have missed the original question, but the significance of
VdW interactions in general should hugely depend on the context.
Let's say, I would expect VdW in protein interfaces to have little
effect, because it gets compensated, on average, by VdW with water
molecules in dissociated state. This effect is known for hydrogen
bonding as well, there was once a discussion whether HBs in interfaces
are actually stabilizing or not.
Eugene.
On Wed, 15 Jul 2009, Nadir T. Mrabet wrote:
Totally agree with what you write.
Yet, I was only answering the question asked (that dealt mostly with
"van Der Waals contacts and effective contacts").
At a time of crisis (DeltaG = only a few kcal/mol), I would say 0.6 kcal/mol
would be a little more than negligible. Question of balance.
Nadir
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: nadir.mra...@medecine.uhp-nancy.fr
Bernhard Rupp wrote:
It might be worthwhile to consider the energy column in the pdf:
At RT we have about 0.6 kcal/mol thermal energy, so a
*single attractive* vdW interaction has little impact - it is generally the
sum of many of those contributing to
notable and important attractive forces. For a *single repulsive* (steep
branch) vdW this is
quite different - your quickly get energetically significant repulsions
even for one bad contact. So the vdW repulsion are both useful (nearly
independent) stereochemical restraints and a good indicator for improbable
conformations (see molprobity clash score, rama, etc).
BR
-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nadir
T. Mrabet
Sent: Wednesday, July 15, 2009 7:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Van der Waals contacts
This issue is far from being trivial.
To address the question, I recommend looking at this simple example
(attached pdf file) which shows that even when the atom distance is twice
the vdw diameter, there is still attraction between atoms (unified type,
with implicit H atoms).
Some, but not all, consider that water screens out interactions, that is,
the vdw interaction is attractive provided that R < Rm + 2 x R(H2O).
But then, one may also need to consider the special case of water-mediated
H-bonds, where the heavy atoms being considered are polar.
HTH,
Nadir
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: nadir.mra...@medecine.uhp-nancy.fr
Cell.: +33 (0)6.11.35.69.09
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Clayton, Gina Martyn wrote:
Hi CCP4ers
Perhaps I am hashing over old news...but
We are having a discussion about Van Der Waals contacts and effective
contacts i.e. the "real distance" of a VDW bump between say a CH and a CH
group which sometimes is described as between a C and a C as i.e.
2x 1.6A and ending about 4A but not including hydrogen.
Some programs list contacts, to say a ligand, as far as 6A apart and some
of the simulation programs use that distance too for contacts for protein
protein interactions.
Does anyone know of a good paper that discusses the effective distance or
has a comment on where a VDW force may begin and end or it's effective
distance - though some say it never truly ends just approaches zero...
G
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