Hi,
I think what you want is to use the 'solventdonor' and
'solventacceptor' keywords. Also the 'nointramol' keyword if you're
not interested in intramolecular hydrogen bonds. So e.g.
hbond res123_solute_hbonds :123 solventdonor :WAT solventacceptor
:WAT.O nointramol avgout res123_solute_hbonds.dat
Hope this helps,
-Dan
On Tue, Feb 5, 2019 at 9:29 AM Rosellen, Martin
<martin.rosellen.16.ucl.ac.uk> wrote:
>
> Hi,
>
> I want to analyse hbonds between a selected residue and water. I follow the "Hydrogen bond analysis with CPPTRAJ" tutorial but have troubles defining the correct mask. How I think it should work is (selected residue 123):
>
> hbond res123_solute_hbonds :123,WAT avgout res123_solute_hbonds.dat
>
> This gives me:
>
> HBOND: Searching for Hbond donors/acceptors in region specified by :123,WAT
> Distance cutoff = 3.000, Angle Cutoff = 135.000
> Writing Hbond avgs to res123_solute_hbonds.dat
> > go
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: WT.prmtop, 221576 atoms, 71504 res, box: Trunc. Oct., 70925 mol, 70919 solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: 'WT.inpcrd' is an AMBER restart file, no velocities, Parm WT.prmtop (Trunc. Oct. box) (reading 1 of 1)
> Coordinate processing will occur on 1 frames.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'WT.prmtop' (1 actions):
> 0: [hbond res123_solute_hbonds :123,WAT avgout res123_solute_hbonds.dat]
> Set up 3 acceptors:
> Set up 2 donors:
> Imaging off.
> Estimated max potential memory usage: 0.456 kB
> ----- WT.inpcrd (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
> TIME: Avg. throughput= 78.7216 frames / second.
>
> ACTION OUTPUT:
> HBOND: Actual memory usage is 0.000 kB
> 0 solute-solute hydrogen bonds.
>
> DATASETS (1 total):
> res123_solute_hbonds[UU] "res123_solute_hbonds[UU]" (integer), size is 1
>
> DATAFILES (1 total):
> res123_solute_hbonds.dat (Avg. solute-solute HBonds)
>
> RUN TIMING:
> TIME: Init : 0.0001 s ( 0.75%)
> TIME: Trajectory Process : 0.0127 s ( 96.83%)
> TIME: Action Post : 0.0001 s ( 0.57%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0001 s ( 0.88%)
> TIME: Other : 0.0001 s ( 0.01%)
> TIME: Run Total 0.0131 s
> ---------- RUN END ---------------------------------------------------
> >
>
> The datafile contains nothing but the header line.
>
> How to correctly specify donors and acceptors?
>
> best
> Martin
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Received on Tue Feb 05 2019 - 09:00:02 PST
