Hi,
the plan was to achieve data about the count of how many OXY molecules are surrounding the residue 1639 within 3 and 5 angstroms cut-off (1st and 2nd solvation shells) and report such data in histograms in order to have a better representation of the mentioned quantities then.
But shall I suppose I am making a wrong use of the multihist command?
What's the best way to retrieve such watershell data?
I've had a different experiment then: I noticed that the output file contains just zeros if I use the solventmask :OXY, whilst if I run a normal watershell command without specifying any solvent (and without stripping the trajectories by water molecules), the output file looks reasonable.
Do I have to think that this is not the way I can achieve such information?
If this is the case, how can I estimate the number of oxygen molecules around my residue during a simulation?
Thanks,
Damiano
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: 26 August 2016 19:11
To: AMBER Mailing List
Subject: Re: [AMBER] Multihist in watershell command
Hi,
On Fri, Aug 26, 2016 at 8:26 AM, Damiano Spadoni
<enxds6.nottingham.ac.uk> wrote:
> 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.
Since you did not specify a min or max for your histogram they are
automatically determined from your data set. The apparent range for
each is 0-1, and since the 'watershell' command counts number of
molecules this means that each data set contains either 0 or 1. The
way that histograms are calculated in cpptraj are 'min <= value <
max', so the max of '1' cannot actually be binned in this case. To bin
it you'd need a max that was just above 1.0 (1.00001 etc).
That said, given that your data sets only have values of 0 or 1
(indicating that at most only 1 OXY is in the vicinity of residue 1639
over the course of this trajectory) it doesn't seem like a histogram
will tell you much in this case.
Hope this helps,
-Dan
> 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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--
-------------------------
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
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This message and any attachment are intended solely for the addressee
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Please do not use, copy or disclose the information contained in this
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University of Nottingham.
This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
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Received on Wed Aug 31 2016 - 09:00:03 PDT
