ok. now i understand. Thank you very much.
Sir,
suppose there is a hydrogen bond ( between a receptor and ligand) which
exists < 5% of the simulation as per trajectory analysis. If a snapshot
extracted ( lowest energy or a representative structure from the most
populated structure) , contained that bond : should it be considered
insignificant and ignored. In biomolecular systems both strong and weak
hbonds play important roles. isnt?
On Fri, Nov 7, 2014 at 6:32 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, 2014-11-07 at 15:57 +0530, Mary Varughese wrote:
> > sir,
> >
> > As per this link
> > http://archive.ambermd.org/201007/0681.html
> >
> > ""atom# :res.atom atom# :res.atom atom# :res.atom %occupied
> > > distance angle lifetime maxocc
> > > | 115 :1.O10 | 104 :1.H20 92 :1.O8 | 96.06 2.818 ( 0.21)
> > > 34.14 (28.58) 45.5 ( 72.3) 390 |....x.
> > > .*..*...........*.x*...**.**.........*.....|
> >
> > The h-bond is formed for 96% of the simulation; average distance of 2.818
> > A with a 0.21 stddev. The lifetime is 45.5 frames (i.e. if you assume 1
> > ps between frames, the average lifetime of the h-bond is 45.5 ps; note
> > that this value will depend on the distance cutofff). Finally the maxocc
> > represents the longest time an h-bond was formed was 390 frames. You can
> > likely see this as fluctuations in the distance > the h-bond cutoff
> > specified. --tec3 ""
> >
> > when its said the bond is there for 96% of the simulation,; what's
> > about such low values like 45.5 frmaes and 390 frames? its reallly
> > confusing
> > would you pls clear it .
>
> What Tom was describing there is a so-called "lifetime" for the hydrogen
> bond, which is a measure of how long the hydrogen bond persists once it
> is formed during the simulation.
>
> Hydrogen bonds are readily made, broken, and remade during the course of
> a simulation. What this measure means is that, on average, this
> hydrogen bond (which exists 96% of the simulation), persists for about
> 45.5 picoseconds (45.5 frames, with each frame being 1 ps apart) before
> breaking (and later reforming).
>
> The _longest_ time this hydrogen bond ever lasted was 390 frames (or 390
> ps) before breaking (and, again, later reforming).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 08 2014 - 09:30:03 PST
