Thanks Dan!
I'm not sure only if I selected mask for the solvent properly but it
produced good graph. Taking into account that :MOL is the ligand within the
cavity and I'd like to estimate water influx exactly into the cavity during
md simulation what reasonable lower and upper cutoffs might be?
watershell :MOL W1.dat :WAT lower 3.0 upper 5.0
PARM [protein.parm7]: Setting up 1 actions.
0: [watershell :MOL W1.dat :WAT lower 3.0 upper 5.0]
Mask [:MOL] represents 46 atoms
Mask [:WAT] represents 25560 atoms
WATER SHELL: Output to W1.dat
The first shell will contain water < 3.000 angstroms from
the solute; the second shell < 5.000 angstroms...
The solute atoms are :290
The solvent atoms are :396-8914,:8915.O,:8915.H1,:8915.H2
James
2015-02-03 17:12 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> Not sure this is exactly what you're looking for, but you might want
> to check out the 'watershell' command, which will record the number of
> water molecules in the 1st and 2nd solvation shells defined by a lower
> cutoff (default 3.4 Ang.) and an upper cutoff (5.0 Ang). This will
> produce a file containing Frame number, # lower, and # upper. You
> could then calculate a histogram which shows where each value peaks
> and use a second run with the 'closest' command to generate
> trajectories containing the first and second or just the first
> solvation shells for further calculation/visualization etc. For
> example:
>
> parm myparm.parm7
> trajin mycrd.nc
> watershell :MOL W1.dat W1 lower 3.0 upper 5.0
> multihist W1[*] out W1.hist.agr bins 50
>
> Hope this helps,
>
> -Dan
>
> On Tue, Feb 3, 2015 at 8:54 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > Dear Amber users!
> >
> > I'm looking for the possibility to calculate number of the water
> molecules
> > detected within the protein (here I define area of interests as :MOL)
> > during molecular dynamic simulation. As the result it will be better to
> > obtain some graph as well showing dependence of the water within 3 A of
> Mol
> > on Y and time on X. Some time ago I did it using some vmd script which
> was
> > lost :) so not I'm looking for another possibility to do this kind of
> > analysis using cpptraj.
> >
> > I'd be thankful for any help,
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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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>
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Received on Tue Feb 03 2015 - 09:00:03 PST
