Dear all!
One extra question regarding analysis of the internal protein's hydration.
Is it possible to gain some insight about kinetics properties (for instance
to estimate residence time of the individual water molecules detected
within the protein) of the water flux during simulation? For my particular
case I've obtained visualization of the water density within the protein
using grid tool in several systems (which differs in the ligand bound to
the protein for instance) and know would like to see how the water flux
could be altered in each of the systems focused on its kinetics as one of
the possibility.
Thanks for suggestions,
James
2015-02-13 10:50 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Feb 25 2015 - 07:30:02 PST
