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
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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)
>>> >> >>>
>>> >> >>> _______________________________________________
>>> >> >>> AMBER mailing list
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>>> >> >>> 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
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>>> >>
>>> > _______________________________________________
>>> > AMBER mailing list
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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)
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
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--
-------------------------
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 Thu Feb 12 2015 - 08:30:03 PST
