AMBER Archive (2005)

Subject: Re: AMBER: about the %occupied of hydrogen bond

From: haixiao jin (jinhx952_at_gmail.com)
Date: Mon Sep 19 2005 - 10:17:31 CDT

thank your patience! :)

On 9/19/05, Carlos Simmerling <carlos.simmerling_at_stonybrook.edu> wrote:
>
> Like I said before, I do not think it is possible to determine the overall
> %
> just from the individual %s. You will need to look at each Hbond vs time
> and
> calculate how often either one is present. Adding them overcounts if you
> have
> both at one time.
>
> haixiao jin wrote:
>
> > 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_at_stonybrook.edu
> > <mailto:carlos.simmerling_at_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_at_stonybrook.edu
> > <mailto:carlos.simmerling_at_stonybrook.edu>
> > > <mailto:carlos.simmerling_at_stonybrook.edu
> > <mailto:carlos.simmerling_at_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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