OK. Keep me informed. The energy calculation that Jmol uses in general for
hydrogen bond calculation is specific to carbonylCO-amideNH interactions and
looks like the following. I'm sorry I don't have a literature reference to
this. If you know it, please let me know -- I'd like to add that as a
comment to the code. I remember some time back having to modify it, though,
because it had some failures. I can't remembe at this moment exactly what I
had to change. So it's not exactly what is published, I think.
The formula is:
QConst = -332 * 0.42 * 0.2 * 1000
energy = (QConst / distOH - QConst / distCH)
+ (QConst / distCN - QConst / distON)
isHbond = (distCN2 > distCH2 && distOH <= 3.0f && energy <= -500)
which is basically just a little formal charge electrostatic
repulsion/attraction approximation putting +1 charge at C and H and -1
charge at O and N.
Bob
from
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java?view=markup
private final static double QConst = -332 * 0.42 * 0.2 * 1000;
private int calcHbondEnergy(Atom nitrogen, Point3f nitrogenPoint,
Point3f hydrogenPoint, AminoMonomer target) {
Point3f targetOxygenPoint = target.getCarbonylOxygenAtomPoint();
float distON2 = targetOxygenPoint.distanceSquared(nitrogenPoint);
if (distON2 < minimumHbondDistance2)
return 0;
float distOH2 = targetOxygenPoint.distanceSquared(hydrogenPoint);
if (distOH2 < minimumHbondDistance2)
return 0;
Point3f targetCarbonPoint = target.getCarbonylCarbonAtomPoint();
float distCH2 = targetCarbonPoint.distanceSquared(hydrogenPoint);
if (distCH2 < minimumHbondDistance2)
return 0;
float distCN2 = targetCarbonPoint.distanceSquared(nitrogenPoint);
if (distCN2 < minimumHbondDistance2)
return 0;
double distOH = Math.sqrt(distOH2);
double distCH = Math.sqrt(distCH2);
double distCN = Math.sqrt(distCN2);
double distON = Math.sqrt(distON2);
int energy = (int) ((QConst / distOH - QConst / distCH + QConst / distCN
- QConst
/ distON));
boolean isHbond = (distCN2 > distCH2 && distOH <= 3.0f && energy <=
-500);
return (!isHbond ? 0 : energy < -9900 ? -9900 : energy);
}
Jmol creates up to two hydrogen bonds to a
On Fri, Nov 7, 2008 at 3:16 AM, David Leader <[EMAIL PROTECTED]> wrote:
>
>
> Bob wrote:
>
> Sure, but -- you said you had the H atoms.... Are you saying you might want
> to move them?
>
>
> On Thu, Nov 6, 2008 at 11:01 AM, David Leader <[EMAIL PROTECTED]
> >wrote:
>
>
> However I still might see if there is a student up to integrating the C
> code. My colleague tells me that this is quite sophisticated. For example
> it
> calculates the H atoms and deals with the uncertainty in serines and
> threonines, by considering three possible rotamers.
>
> David
>
>
> Sure, for my immediate purposes with the proteins I have the connect script
> might be ok (haven't got it working yet, but I'm busy teaching and watching
> football at the moment), but in the long term for general use a function
> that calculates the protein H-bonds properly (ie calculates energies, as our
> program does) would be of general benefit. Any student working on it
> wouldn't start properly until next May, so it's longer term. However I need
> to suggest a project by the end of next week - hence my query.
> I certainly will look at the connect script over the weekend and get back
> to you if necessary.
>
> David
>
> ___________________________________________________
>
> Dr. David P. Leader, Faculty of Biomedical & Life Sciences,
> University of Glasgow, Glasgow G12 8QQ, UK
> Phone: +44 (0)141 330 5905
> http://doolittle.ibls.gla.ac.uk/leader
> http://motif.gla.ac.uk/
>
> The University of Glasgow, charity number SC004401
> ___________________________________________________
>
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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