From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat May 21 2016 - 18:44:09 CDT
There’s a few factors at play here, the main one being lack of polarization. Beta sheets in particular can not reproduce the correct geometry of hydrogen bonds in a fixed-charge force field (at least that’s what I recall).
Here’s a recent paper that seems especially relevant: http://pubs.acs.org/doi/abs/10.1021/jp503972j <http://pubs.acs.org/doi/abs/10.1021/jp503972j>
> On May 20, 2016, at 5:18 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> H-bonds in the charmm-ff are substantially viewed as in the excerpts below:
> From: Tim Isgro (timisgro_at_ks.uiuc.edu <mailto:timisgro_at_ks.uiuc.edu?Subject=Re:%20%20hydrogen%20bonds%20in%20NAMD>)
> Date: Fri Mar 19 2004 - 11:25:47 CST
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> Hi Ioana,
> The hydrogen bond potential in the Charmm force field is, from what I
> gather, viewed skeptically by many people, since there is no very good way
> to benchmark the parameters and potential.
> From: Axel Kohlmeyer (akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com?Subject=Re:%20%20question%20on%20hydrogen%20bond>)
> Date: Mon Sep 06 2010 - 04:08:32 CDT
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> On Sun, Sep 5, 2010 at 11:40 PM, Kwee Hong <joyssstan0202_at_gmail.com <mailto:joyssstan0202_at_gmail.com?Subject=Re:%20%20question%20on%20hydrogen%20bond>> wrote:
> > Hi.
> > In the namd-tutorial-unix.pdf, it mentioned that explicit hydrogen bond
> > terms are no longer present in the CHARMM force field and are therefore not
> > calculated by NAMD. Does this mean that throughout the simulation, hydrogen
> > bonding are not calculated? So does that mean that I can't inspect the
> hydrogen bonds are a phenomenological description and thus
> technically a not an easily identifiable term for a force field.
> they are more a "side effect" of the charge distribution and
> geometry of groups involving hydrogens bound to certain atoms
> (h-bond donors) and their counter parts (h-bond acceptors
> Be that as it may be, is charmm36, as run with namd2.11 for a protein in TIP3 water solution, capable of maintaining all distances between aa O-atoms with interposed H atom, as determined by X-ray diffraction of the protein crystal? When not (as I am observing), should one suspect that the fictitious charge distribution was incorrectly calculated? Or simply assume that crystal and water solution are different affairs? Which would imply that crystallographers should refrain from making too many conclusions from their structural data.
> Grateful for a recent point of view.
> francesco pietra
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