Thank you. Now it is much clearer.
I have one more question about lifetime analysis. I've tried
hbond bond1 out nhb1.dat :1-342 dist 3 series donormask
:204&!.CA,CB,C|:342.O acceptormask :204.OD1,OD2|:342.O avgout avghb1.dat
solventdonor :WAT.O solventacceptor :WAT.O bridgeout bridge1.dat solvout
solvent1.dat
lifetime lifeout bond1
But I get
Error: lifetime: No data sets selected.
Error: Could not setup analysis [lifetime]
What am I doing wrong here?
Fabrício
2013/10/30 Daniel Roe <daniel.r.roe.gmail.com>
> Hi,
>
> On Wed, Oct 30, 2013 at 12:34 PM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
> > with cpptraj. I have specified the analysis along with the options for
> > solvent hbond analysis and bridge. Within the hbond between residues, the
> > interaction between a carboxylate from an asp residue and the hydrogens
> > from the guanidinium group show up like this:
> > ASP_204.OD2 ARG_206.HE ARG_206.NE 4228 0.8456
> 3.0151 145.4176
> > ASP_204.OD1 ARG_206.HE ARG_206.NE 4072 0.8144
> 3.2199 154.9778
> > So, the fraction of frames in which OD2 and OD1 stay bonded to the same
> > hydrogen atom on arginine is 0.8456 and 0.8144 respectively. How can this
> > be so? Shouldn’t the fractions add up to 1?
>
> Remember that hbond is essentially an enhanced version of the
> 'distance' command, subject to distance and angle cutoffs. Any time
> those distance and angle criteria are satisfied, a hydrogen bond is
> considered "formed". It's entirely possible that for certain frames,
> OD1 and OD2 are close enough to HE satisfy your distance and angle
> cutoffs at the same time (you don't specify what your cutoffs were but
> I'm assuming at least 3.3 for distance?). Because of this they don't
> necessarily have to add up to 1.0.
>
> > I get even more confused when I take into account the other interactions
> > that this asp residue does.
> > ASP_204.OD2 OH1_342.H1 OH1_342.O 4612 0.9224
> 2.9481 158.4453
> > This is OD2 bonded to a water molecule bound to a zinc complex.
> > In the solvent analysis output.
> > OH1_342.O SolventH SolventDnr 10182 2.0364
> > 2.7305 162.2674
> > How can the Hbond appear in 10182 frames if I only analysed 5000?
>
> The hbond section (8.10.18) of the AT13 manual explains this:
>
> "If solvout is specified the average of each solute-solvent hydrogen
> bond formed over the course
> of the trajectory will be written to <sfilename> in a manner analogous
> to avgout. Note that for
> solute-solvent hydrogen bonds the ’Frames’ column becomes ’Count’
> since for any given
> frame more than 1 solvent molecule can bind to the same place on
> solvent and vice versa."
>
> So it's likely that there were ~2 solvent molecules in the vicinity of
> that OH1_342.O atom.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Wed Oct 30 2013 - 13:30:03 PDT
