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
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> 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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Received on Tue Feb 17 2015 - 10:00:02 PST
