... and here what I've got from the Amber-tools14 using 'bounds' command
ACTION OUTPUT:
4.804949 < X < 83.057938
0.951227 < Y < 36.727116
42.903404 < Z < 78.433228
GRID: grid max is 328.000
now should I use from that output only maximum dimensions: 83.057938
36.727116 78.433228 for the grid calculations still being centered on the
area of interest for which those XYZ have been obtained?
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?
# 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
>>
>
>
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Received on Tue Feb 10 2015 - 11:00:02 PST
