This is exactly what I was looking for. Thanks a lot, Daniel!
On Tue, Feb 17, 2015 at 12:45 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The solventdonor/solventacceptor keywords are designed to be
> non-specific. To track specific waters you will need to consider them
> as "solute". Be aware though that when tracking individual waters the
> bookkeeping can become a bit of a nightmare since you have to track
> every solvent molecule as an individual potential donor/acceptor. For
> even small-sized systems this will become quite memory hungry for
> longer trajectories (less so if you're focusing on a specific region
> of your solute, but still pretty demanding), not to mention slow. I
> think the way you have to do this is via two 'hbond' commands, one
> where you look at solvent donor/solute acceptor, and the other where
> you look at solvent acceptor/solute donor, like so:
>
> hbond hb_1_wat out hb_1_wat.dat avgout avg1.dat series donormask :1
> acceptormask :WAT.O
> hbond hb_wat_1 out hb_wat_1.dat avgout avg2.dat series donormask :WAT
> acceptormask :1
>
> Then you will end up with two groups of data sets (hb_1_wat[solutehb]
> and hb_wat_1[solutehb]) that you can then feed to 'lifetime'. The
> reason you have to use two hbond commands is otherwise you will be
> tracking solvent-solvent hydrogen bonds as well, which will straight
> up devour your memory.
>
> Anyway, hope this helps,
>
> -Dan
>
> PS - Just out of curiosity, why not just use 'lifetime' analysis on
> the resulting H1[solventhb] data sets?
>
>
> On Tue, Feb 17, 2015 at 8:57 AM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > Dear amber gurus,
> >
> > I am looking into hbond but I can't figure out how to report the identity
> > of the water molecules that participate of H-bonds with the protein.
> Thus,
> > I have no way to find out about the lifetimes of solute-solvent bonds.
> >
> > My hbond command (protein residues from 1 to 215):
> > hbond H1 out hbond.dat (:1-215)&(.N*,.H*,.O*) series avgout avgout.dat
> > printatomnum nointramol solventdonor :WAT&.O solventacceptor :WAT&.O
> > solvout solvout.dat bridgeout bridgeout.dat
> >
> > The first lines of solvout.dat:
> > #Solute-Solvent Hbonds:
> > #Acceptor DonorH Donor Count Frac
> > AvgDist AvgAng
> > ASP_197.OD1_2876 SolventH SolventDnr 3 3.0000 2.6282
> 172.8679
> > ASP_74.OD2_1084 SolventH SolventDnr 3 3.0000 2.6591
> 163.7221
> >
> > The file reports the atoms in the protein participating of the H-bonds,
> but
> > there is no atomic info for the solvent molecules. How can I change this?
> >
> > Thanks in advance
> > Jose Borreguero
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 17 2015 - 13:00:03 PST
