'multihist' is a cpptraj command. The input I provided should work as
a cpptraj script.
-Dan
On Wed, Feb 4, 2015 at 2:30 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 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 - 08:30:02 PST
