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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Received on Wed Feb 04 2015 - 02:00:03 PST
