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 - 07:00:02 PST
