Ok. thank you for this helpful suggestion.
> I've done calculations such as this on a number of occasions. The
> procedure we used was roughly the following.
>
> 1) Run MD and define all bound and unbound simulation frames
> 2) either prevent the rotation and translation of the host or align them
> after the simulation is done.
> 3) define a volume (we usually use a rectangular polyhedra) for which the
> ligand is inside the cube for all bound configurations. We tend to use
> autodock tools to visualize the origin and dimensions of this region.
> 4) calculate the average number of water molecules in the cube for bound
> configurations compared to unbound configurations and take the difference.
>
> For step four, we usually use cpptraj (gist) and GistPP (Gist post
> processing tools) however this is overkill for just the number of water
> molecules in the region since GIST comes with the baggage of the expensive
> calculations The grid command in cpptraj should give the same
> information
> and run significantly faster.
>
> Also, you should play with the dimensions of the rectangular polyhedra and
> make it large enough such that the resulting difference in waters in the
> region between the bound and unbound configuration is insensitive to the
> dimensions.
>
> Tom
>
>
>
> On Mon, May 7, 2018 at 11:22 AM, Tousif Hossen
> <tousif.hossen.iitg.ernet.in>
> wrote:
>
>>
>> ok. thank you for this useful information.
>>
>>
>> > I think you're misunderstanding how closest works- closest doesn't
>> operate
>> > on a distance cutoff, but a numerical cutoff from the number of water
>> > molecules, ie
>> >
>> >
>> > closest 10 :1
>> >
>> >
>> > is taking in the ten closest water molecules regardless of how far
>> away
>> > they are. If you want to know within a distance cutoff, you'll have to
>> use
>> > watershell instead.
>> >
>> >
>> > Best,
>> >
>> >
>> > Kenneth
>> >
>> > ________________________________
>> > From: Tousif Hossen <tousif.hossen.iitg.ernet.in>
>> > Sent: Monday, May 7, 2018 9:38:35 AM
>> > To: amber.ambermd.org
>> > Subject: Re: [AMBER] calculation of cavity water
>> >
>> >
>> >
>> >
>> >
>> >> Actually in my case, 'closest' command taking into account 10
>> > angstrom from the ring of the cyclodextrin, not from center
>> > of CD.
>> > I have tried with
>> > closest 10 :1
>> > or closest 10 :CD
>> > but if I use 'closest 10 :1.CD', it is considering whole simulation
>> box.
>> >
>> >
>> >>
>> >> thank you for such helpful information.
>> >>
>> >>> Hi,
>> >>>
>> >>>
>> >>> closest by default only picks up on the closest (distance based)
>> water
>> >>> molecule to a mask- ie,
>> >>>
>> >>>
>> >>> closest 10 :2.CD1
>> >>>
>> >>>
>> >>> will produce the closest 10 waters, etc. Because closest doesn't
>> >>> actually
>> >>> take into account how far the waters are, and only cares about the
>> >>> number
>> >>> of waters to grab, you have to run the watershell command first to
>> get
>> >>> a
>> >>> rough idea of how many waters are around your mask.
>> >>>
>> >>>
>> >>> Best,
>> >>>
>> >>>
>> >>> Kenneth
>> >>>
>> >>> ________________________________
>> >>> From: Tousif Hossen <tousif.hossen.iitg.ernet.in>
>> >>> Sent: Sunday, May 6, 2018 2:29:43 AM
>> >>> To: AMBER Mailing List
>> >>> Subject: Re: [AMBER] calculation of cavity water
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> i have used closest command. but it is showing close water molecule
>> >>> outside the cavity.
>> >>>
>> >>>> To the extent of my knowledge, the 3D reference interation site
>> model
>> >>>> theory proves to be more accurate in calculating the number of
>> water
>> >>>> molecules inside cavity.
>> >>>> The 3D RISM calculations can be done in AMBER. However, you need to
>> >>>> check
>> >>>> out whether it can be implemented for your system or not.
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Sat, May 5, 2018 at 1:45 AM, Kenneth Huang
>> >>>> <khuang8.student.gsu.edu>
>> >>>> wrote:
>> >>>>
>> >>>>> Hi,
>> >>>>>
>> >>>>>
>> >>>>> You might want to check out a combination of the watershell and
>> >>>>> closest
>> >>>>> commands in cpptraj.
>> >>>>>
>> >>>>>
>> >>>>> Best,
>> >>>>>
>> >>>>>
>> >>>>> Kenneth
>> >>>>>
>> >>>>>
>> >>>>> ________________________________
>> >>>>> From: Tousif Hossen <tousif.hossen.iitg.ernet.in>
>> >>>>> Sent: Friday, May 4, 2018 7:11 AM
>> >>>>> To: amber.ambermd.org
>> >>>>> Subject: [AMBER] calculation of cavity water
>> >>>>>
>> >>>>>
>> >>>>> Hi AMBER community,
>> >>>>> Currently I am working on host-guest system with
>> >>>>> beta-cyclodextrin. I want to calculate the number of
>> >>>>> water molecules inside cavity in presence of guest and
>> >>>>> also in absence. However, I am not getting any idea how
>> >>>>> to calculate this? please help me and suggest some idea.
>> >>>>> Thank you in advance.
>> >>>>>
>> >>>>> --
>> >>>>> Tousif Hossen
>> >>>>> Research Scholar
>> >>>>> Department of Chemistry
>> >>>>> IIT GUWAHATI
>> >>>>> INDIA
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> AMBER mailing list
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>> >>>>> 7C704d822c358a47849a1649e20b75f941%7C0%7C0%
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>> 7Ckhuang8%40student.gsu.edu%7Ca5704af346544aae019b08d5b31af51a%
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>> >>>>>
>> >>>> _______________________________________________
>> >>>> AMBER mailing list
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>> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%
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>> >>>>
>> >>>
>> >>>
>> >>> --
>> >>> Tousif Hossen
>> >>> Research Scholar
>> >>> Department of Chemistry
>> >>> IIT GUWAHATI
>> >>> INDIA
>> >>>
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> https://na01.safelinks.protection.outlook.com/?url=
>> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%
>> 7Ckhuang8%40student.gsu.edu%7Ca5704af346544aae019b08d5b31af51a%
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>> 1gJjfWNBgGO4OsgT1dY%2FCsXeuuAvLTAgOo70BxBOf3c%3D&reserved=0
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> https://na01.safelinks.protection.outlook.com/?url=
>> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%
>> 7Ckhuang8%40student.gsu.edu%7C9603d30faf244de0ca9608d5b41ff6fa%
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>> >>>
>> >>
>> >>
>> >> --
>> >> Tousif Hossen
>> >> Research Scholar
>> >> Department of Chemistry
>> >> IIT GUWAHATI
>> >> INDIA
>> >>
>> >
>> >
>> > --
>> > Tousif Hossen
>> > Research Scholar
>> > Department of Chemistry
>> > IIT GUWAHATI
>> > INDIA
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > https://na01.safelinks.protection.outlook.com/?url=
>> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%
>> 7Ckhuang8%40student.gsu.edu%7C9603d30faf244de0ca9608d5b41ff6fa%
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>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --
>> Tousif Hossen
>> Research Scholar
>> Department of Chemistry
>> IIT GUWAHATI
>> INDIA
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ************************************************
> Tom Kurtzman, Ph.D.
> Associate Professor
> Department of Chemistry
> Lehman College, CUNY
> 250 Bedford Park Blvd. West
> Bronx, New York 10468
> 718-960-8832
> http://www.lehman.edu/faculty/tkurtzman/
> <http://www.lehman.edu/faculty/tkurtzman/index.html>
> ************************************************
> _______________________________________________
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>
--
Tousif Hossen
Research Scholar
Department of Chemistry
IIT GUWAHATI
INDIA
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Received on Mon May 07 2018 - 11:30:03 PDT
