thank you for your kind help! yes, in the particular case, the %occupied
between O6 and OD1 has already reached 98.4%, it does not need to know the
total %occupied. however, in the first case,
atom
residue
distance
%occupied
WAT471-O(H1)
ASP220 (OD2)
2.697
55.20
WAT471-O(H2)
ASP220 (OD2)
2.689
44.60
what is the total %occupied of H-bond between Wat471 and ASP220? is the
total %occupied (55.20+44.60)? is the distance (2.697*55.20+2.689*0.446)/(
55.20+44.60)?
On 9/19/05, Carlos Simmerling <carlos.simmerling.stonybrook.edu> wrote:
>
> that's what I thought, so look at my original suggestion (Hbond vs time
> for
> each). you'll need to postprocess the data or find a different program.
> in the particular case that you mention do you really need to know the
> total % if the ID1 is already 98.4%? That is almost all of the time.
> Unless you are very sure that your data is well converged and independent
> of initial conditions, you probably have uncertainties larger than +/-1.6%
> anyway.
>
>
>
> haixiao jin wrote:
>
> > thank youfor your help! i should make my question more clear.
> > i calculated the H-bond occupied by PTRAJ in AMBER. the cutoff of
> > distance and angle of hydrogen bond is 3.5 and 120.0, respectively.
> > i know the mean of "%occuped" between two atoms, for example, the
> > %occupied between the O6 of ligand and the OD1 of ASP184 is 98.4%. it
> > is presents the percentual fraction of existence of the hydrogen bond
> > out of the total time of simultaion is 98.4. but there also exist the
> > hydrogen bond between the O6 and the OD2 of ASP184. so, how can we
> > express the total %occupied of H-bond between O6 and ASP184?
> >
> >
> >
> > On 9/16/05, *Carlos Simmerling* <carlos.simmerling.stonybrook.edu
> > <mailto:carlos.simmerling.stonybrook.edu>> wrote:
> >
> > maybe the original question is how to determine the % of time
> > these two
> > GROUPS
> > are hydrogen bonded, and ptraj gives the % for the specific atom
> > pairs.
> >
> > For example, if the two atom pairs are H-bonded 50% each, it could
> > be that
> > 50% of the time there is a bifurcated Hbond and 50% no Hbond, or
> > it could be that It is 1 Hbond in 50% and the other in 50%, so 100%
> > of the time there is an Hbond between the groups. There just isn't
> > a way
> > to tell that from the average data, you'll need to do some
> > processing of
> > the
> > Hbonds vs time and see how often you have at least 1 of them.
> >
> > If this isn't what you meant, please try to clarify exactly what you
> > want to calculate.
> >
> >
> > Thomas E. Cheatham, III wrote:
> >
> > >>I have gotten the hydrogen bond occupied. But in the followed
> > two example, I
> > >>don't know how to express the %occupied.
> > >>
> > >>atom
> > >>
> > >>residue
> > >>
> > >>distance
> > >>
> > >>%occupied
> > >>
> > >>WAT471-O(H1)
> > >>
> > >>ASP220 (OD2)
> > >>
> > >>2.697
> > >>
> > >>55.20
> > >>
> > >>
> > >
> > >>From the information given, it is not clear where you obtained
> > the data
> > >shown, but if this was the hydrogen bond facility of ptraj, you
> > in the
> > >above observed an average distance (when formed, i.e. < cutoff)
> > of 2.697
> > >angstroms and an occupancy of 55.2% (meaning that it was formed
> > slightly
> > >more than half the time). Occupancies and average distances will
> > depend
> > >on the definition of the h-bond (cutoff distance, angle). If the
> > distance
> > >cutoff is longer, the occupancy may be higher.
> > >
> > >
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Received on Mon Sep 19 2005 - 15:53:03 PDT
