Dear Amber users,
I am trying to analyse the solvation shells of a metal cluster buried in my protein (:1639) using a solvent mask that relates to free oxygen molecules (:OXY) rather than water ones. The simulation produced is about the solvated protein with a specific number of oxygen molecules free to move inside the whole system.
This is the script I feed to cpptraj on ambertools16:
parm SAMoy_noWatIons.prmtop
trajin SAMoxy_50nsReimagedNowatIons.nc
watershell :1639 W1_clust1.dat W1 :OXY
multihist W1[*] out W1.hist.gnu bins 100
The trajectories have been stripped from water and counterions and been reimaged.
The problem I am experiencing is with the hist/multihist (I used both, but the results doesn't change) command that seems to be unable to produce any meaningful output files (loads of 0s in them).
Visible warnings are:
ANALYSIS: Performing 1 analyses:
0: [multihist W1[*] out W1.hist.gnu bins 100]
Calculating step from min=0 max=1 bins=100.
Dim W1[lower]: 0.000000->1.000000, step 0.010000, 100 bins.
Hist: 25000 data points in each dimension.
Hist: Allocating histogram, total bins = 100
Warning: Frame 12506 Coordinates out of bounds (100)
Warning: Frame 18054 Coordinates out of bounds (100)
Warning: Frame 18066 Coordinates out of bounds (100)
Warning: Frame 18069 Coordinates out of bounds (100)
Warning: Frame 18071 Coordinates out of bounds (100)
Warning: Frame 18072 Coordinates out of bounds (100)
Warning: Frame 18078 Coordinates out of bounds (100)
Warning: Frame 18082 Coordinates out of bounds (100)
Calculating step from min=0 max=1 bins=100.
Dim W1[upper]: 0.000000->1.000000, step 0.010000, 100 bins.
Hist: 25000 data points in each dimension.
Hist: Allocating histogram, total bins = 100
Warning: Frame 12504 Coordinates out of bounds (100)
Warning: Frame 12506 Coordinates out of bounds (100)
Warning: Frame 12507 Coordinates out of bounds (100)
Warning: Frame 12508 Coordinates out of bounds (100)
..and many others like those.
My questions are: am I doing an incorrect use of multihist command? Is it a so transcendental thing using a different solvent mask for something that is not water?
Any other has seen such warnings?
Any suggestions will obviously be appreciated.
Best regards,
Damiano
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Received on Fri Aug 26 2016 - 05:30:03 PDT
