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)
> >> >>>
> >> >>> _______________________________________________
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> >> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>
> >> >>
> >> >>
> >> > _______________________________________________
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> >> > 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > 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 Tue Feb 10 2015 - 09:30:03 PST
