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
>> >>> >>>>
>> >>> >>>
>> >>> >>>
>> >>> >>
>> >>> > _______________________________________________
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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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>> AMBER mailing list
>> AMBER.ambermd.org
>> 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 Tue Feb 10 2015 - 07:00:02 PST
