Thanks Dan,
I think multhist has not been included yet to the amber-12 which I'm using
...
INPUT: Reading Input from file water.in
[parm ./top_all/7D4-androsta.top]
[trajin ./tr_all/7D4-androsta.mdcrd]
[7D4-androsta.mdcrd] contains 5191 frames.
[watershell :104 W1_apo_DRY.dat :WAT.O* lower 3 upper 5]
[multihist W1[*] out W1.hist.agr bins 50]
Warning: Unknown Command multihist.
James
2015-02-05 17:06 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> The 'grid' command will allow you to calculate water occupancy (not
> yet normalized, although this option is in the next cpptraj release)
> which you can compare between different simulations. However, it's
> probably best to rms-fit the solute (i.e. the protein, not the ligand)
> to a common reference prior to 'grid' to remove rotation/translation
> of the solute. In other words, you want to view water occupancy with
> your protein as the frame of reference.
>
> -Dan
>
> On Thu, Feb 5, 2015 at 2:24 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > (+) How do you think will it be better to use grid command (in comparison
> > to watershell) from the cpptraj to compare probability of the water
> > distribution throughout the protein interior during several md runs? In
> > general watershell gave me satisfied results but I'd like to obtain more
> > statistical-relevant distribution avoiding with the choosing of proper
> > cut-offs.
> >
> > James
> >
> > 2015-02-04 10:30 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> >
> >> Could you also provide me with the link where is possible to download
> >> multhist tool? As I realize it might be some python script which I had
> not
> >> find in my amber12. IS it possible to plot such multiple graph values
> >> agains time prolongation using xmgrace?
> >>
> >> Thanks,
> >>
> >> James
> >>
> >> 2015-02-03 17:38 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> >>
> >>> 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)
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>
> > _______________________________________________
> > 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 06 2015 - 00:30:03 PST
