Hi Dan,
thanks alot! Not it's works too.
The question is only how it would be better for the visualization in my
particular case. Using the below script I obtained grid:
# focus on some area of interest
center :272 mass origin
image origin center
#make rmsf fit if it's nessesary
#rms first mass out rms-grid :1-289
trajout md_apo_fit.dcd dcd first last 10 nobox
# calculate grid for the water
grid test.xplor 83.057938 0.5 36.727116 0.5 78.433228 0.5 :WAT.O*
where grid dimensions have been obtained by bonds:
ACTION OUTPUT:
4.804949 < X < 83.057938
0.951227 < Y < 36.727116
42.903404 < Z < 78.433228
GRID: grid max is 328.000
now in VMD it's visually looks like the red slice around of the protein
(with the pereodicity in +Z and -Y!) which include some lipids (!)
besides the water so it seems fully correct for me :)
Gleb
2015-02-12 16:59 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Tue, Feb 10, 2015 at 11:36 AM, James Starlight
> <jmsstarlight.gmail.com> wrote:
> > BTW I also noticed that amber14 has different output format for for grid
> > which has not been recognized as the XPLOR by VMD. How it could be loaded
> > for the visualization?
>
> The .dat extension is generic, so cpptraj defaults to a generic output
> format when that is specified. If you want XPLOR you need to provide a
> file name extension that cpptraj recognizes as XPLOR (.grid or .xplor)
> or explicitly write out the grid data with 'writedata' and the 'xplor'
> keyword.
>
> -Dan
>
> >
> > # GRID_00001
> > 1.000 1.000 1.000 31.0000
> > 2.000 1.000 1.000 33.0000
> > 3.000 1.000 1.000 50.0000
> > 4.000 1.000 1.000 39.0000
> > 5.000 1.000 1.000 43.0000
> > 6.000 1.000 1.000 47.0000
> > 7.000 1.000 1.000 41.0000
> > 8.000 1.000 1.000 48.0000
> > 9.000 1.000 1.000 57.0000
> > 10.000 1.000 1.000 66.0000
> > 11.000 1.000 1.000 59.0000
> >
> > James
> >
> > 2015-02-10 18:23 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> >
> >> Hi Dan,
> >>
> >> Thanks for ideas again! Here what I've done:
> >>
> >> 1) firstly below is my leap script for the visualization of water
> density
> >> using grid (still in amber tools 12)
> >>
> >> # focus on some area of interest- ligand within the receptor's cavirt
> >> center :290 mass origin
> >> image origin center
> >>
> >> #make rmsf fit
> >> rms first mass out rms-grid :4-9,16-21
> >> grid test.dat 100 0.5 100 0.5 100 0.5 :WAT.O*
> >>
> >>
> >> 2)now when I load it to the VMD I didn't see any visualization of water
> >> density although all data has been loaded correctly. Should I switch
> some
> >> option in VMD for that?
> >>
> >> vmd > edmplugin) EOF sentinel != -9999
> >> Info) Analyzing Volume...
> >> Info) Grid size: 100x100x100 (15 MB)
> >> Info) Total voxels: 1000000
> >> Info) Min: 0.000000 Max: 639.000000 Range: 639.000000
> >> Info) Computing volume gradient map for smooth shading
> >> Info) Added volume data, name=test.dat : X-PLOR Electron Density Map
> >>
> >> 3) Is it possible to compare density from several trajectories using
> some
> >> numerical data besides of the visualization?
> >>
> >> James
> >>
> >>
> >> 2015-02-10 15:43 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >>
> >>> On Tue, Feb 10, 2015 at 5:58 AM, James Starlight <
> jmsstarlight.gmail.com>
> >>> wrote:
> >>> > Warning: AMBERHOME [None] differs from expected [/+SOFTWARE/amber12].
> >>> > No changes will be made until this is fixed
> >>> > SetupError: Making changes has been disabled because AMBERHOME is not
> >>> set
> >>> > correctly or the updater has been moved from AMBERHOME.
> >>> >
> >>> > should I remove ambertools folder explicitly from the AMBERHOME and
> >>> install
> >>> > AmberTools14 from the source?
> >>>
> >>> Unless you're hurting for space, you can just extract the AmberTools
> >>> 14 tarball in a separate directory and set AMBERHOME to that. Since
> >>> pmemd is the only non-free program in Amber 14 (and does not need
> >>> AMBERHOME set I believe) you can then leave AMBERHOME set to your
> >>> AmberTools 14 directory. See Jason Swails page for more detailed
> >>> instructions on installing Amber: http://jswails.wikidot.com/#toc10
> >>>
> >>> > 2) Using GRID from amber-tools-12 I've obtained several output.dat
> files
> >>> > for each of the system under analysis - each of whicvh is looks like
> >>> >
> >>> > This line is ignored
> >>> > 1
> >>> > rdparm generated grid density
> >>> > how it would be better to compare it using some visualization in VMD
> for
> >>> > instance?
> >>>
> >>> This format is XPLOR density, which VMD can read.
> >>>
> >>> -Dan
> >>>
> >>> >
> >>> >
> >>> >
> >>> > 2015-02-06 18:52 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >>> >
> >>> >> > I think multhist has not been included yet to the amber-12 which
> I'm
> >>> >> using
> >>> >>
> >>> >> I highly recommend upgrading to AmberTools 14, which is free. It
> >>> >> includes many updates and enhancements over Amber 12, which is
> several
> >>> >> years old at this point.
> >>> >>
> >>> >> On Fri, Feb 6, 2015 at 2:05 AM, James Starlight <
> >>> jmsstarlight.gmail.com>
> >>> >> wrote:
> >>> >> >
> >>> >> > [reference ./protein.pdb]
> >>> >> > Error: ./protein.pdb: No frames read. atom=4542 expected 46488.
> >>> >>
> >>> >> Cpptraj requires topology information to load coordinates, or to put
> >>> >> it another way there must be a 'parm' that can be used with any
> given
> >>> >> 'trajin'. So what you really want is something like:
> >>> >>
> >>> >> parm ../protein.pdb [REFPARM]
> >>> >> reference ../protein.pdb parm [REFPARM]
> >>> >>
> >>> >> Even though 'protein.pdb' contains both topology and coordinate
> >>> >> information, cpptraj doesn't assume you want to use them together,
> the
> >>> >> reason being that you may want to e.g. use that PDB file with a
> >>> >> matching Amber topology file (to get things like bonds, charges,
> etc).
> >>> >>
> >>> >> > (2)
> >>> >> > # here I chose grid dimensions from the XYX of the box vectors
> >>> proding
> >>> >> mask
> >>> >> > of the solvent
> >>> >> > grid grid.dat 60 1 80 1 100 1 :WAT.O*
> >>> >> >
> >>> >> > 1- should I add something else to this conditions in case of my
> task?
> >>> >> > 2- How it would be better to compare several grid.dat output files
> >>> >> produced
> >>> >> > for several trajectories?
> >>> >>
> >>> >> You may want to just focus your grid around the molecule of interest
> >>> >> (in your case I think it was :MOL). The simplest way to do that in
> my
> >>> >> opinion is to upgrade to cpptraj from AmberTools 14 and use the
> >>> >> 'bounds' command, which will provide minimum and maximum XYZ values
> >>> >> for a selection of atoms that you can then use to create a grid.
> Also,
> >>> >> for something like this its probably best to make sure your molecule
> >>> >> of interest and the grid itself are centered at the origin. See the
> >>> >> manual for relevant keywords.
> >>> >>
> >>> >> Hope this helps,
> >>> >>
> >>> >> -Dan
> >>> >>
> >>> >> >
> >>> >> >
> >>> >> > James
> >>> >> >
> >>> >> > 2015-02-06 9:23 GMT+01:00 James Starlight <jmsstarlight.gmail.com
> >:
> >>> >> >
> >>> >> >> 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)
> >>> >> >>>
> >>> >> >>> _______________________________________________
> >>> >> >>> 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)
> >>> >>
> >>> >> _______________________________________________
> >>> >> 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)
> >>>
> >>> _______________________________________________
> >>> 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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Received on Fri Feb 13 2015 - 02:00:02 PST
