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

From: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
Date: Mon, 19 Sep 2005 10:28:19 -0400

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.stonybrook.edu
> <mailto: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>
> > <mailto: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.
> > >
> > >
> >
> >-----------------------------------------------------------------------
> >
> > >The AMBER Mail Reflector
> > >To post, send mail to amber.scripps.edu
> <mailto:amber.scripps.edu> <mailto:amber.scripps.edu
> <mailto:amber.scripps.edu>>
> > >To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu <mailto:majordomo.scripps.edu>
> > <mailto: majordomo.scripps.edu <mailto:majordomo.scripps.edu>>
> > >
> > >
> >
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> <mailto:amber.scripps.edu> <mailto:amber.scripps.edu
> <mailto:amber.scripps.edu>>
> > To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu <mailto:majordomo.scripps.edu>
> > <mailto:majordomo.scripps.edu <mailto:majordomo.scripps.edu>>
> >
> >
>
> -----------------------------------------------------------------------
>
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu <mailto:amber.scripps.edu>
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> <mailto:majordomo.scripps.edu>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Sep 19 2005 - 15:53:04 PDT
Custom Search