Here some question about fitting and grid commands
(1)
# here I choose first frame of one the simulation as the reference
reference ./tr_all/7D4-androsta.mdcrd firstframe
rms reference :1-361.CA out rmsd.dat
The question: is it possible to chose some pdb structure of x-ray structure
consisted of protein only as the refence for all simulations? When I try to
do it in above command I obtained error:
[reference ./protein.pdb]
Error: ./protein.pdb: No frames read. atom=4542 expected 46488.
(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?
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
>> >>>>
>> >>>
>> >>>
>> >>
>> > _______________________________________________
>> > 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
Received on Fri Feb 06 2015 - 01:30:03 PST
