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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Received on Thu Feb 05 2015 - 08:30:03 PST
