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
> >>>>> 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%7C6f4479759dc045707bfd08d5b1b002c0%
> >>>>> 7C704d822c358a47849a1649e20b75f941%7C0%7C0%
> 7C636610291888939612&sdata=
> >>>>> fwBz1j0LO3OXVPsrihStmSPB25B%2BxTo2%2FU0UPXicyrA%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%7Ca5704af346544aae019b08d5b31af51a%
> 7C704d822c358a47849a1649e20b75f941%7C0%7C1%7C636611850747339865&sdata=
> 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%7Ca5704af346544aae019b08d5b31af51a%
> 7C704d822c358a47849a1649e20b75f941%7C0%7C1%7C636611850747339865&sdata=
> 1gJjfWNBgGO4OsgT1dY%2FCsXeuuAvLTAgOo70BxBOf3c%3D&reserved=0
> >>>>
> >>>
> >>>
> >>> --
> >>> 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%
> 7C704d822c358a47849a1649e20b75f941%7C0%7C1%7C636611850747339865&sdata=
> 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%
> 7C704d822c358a47849a1649e20b75f941%7C0%7C1%7C636612971762220977&sdata=
> 8PNbWIrYCAWkucv5wp8OPH9uyqS%2FdHn%2F%2FcLuy0Lj%2BPY%3D&reserved=0
> >>>
> >>
> >>
> >> --
> >> 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%
> 7C704d822c358a47849a1649e20b75f941%7C0%7C1%7C636612971762220977&sdata=
> 8PNbWIrYCAWkucv5wp8OPH9uyqS%2FdHn%2F%2FcLuy0Lj%2BPY%3D&reserved=0
> > _______________________________________________
> > 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>
************************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 07 2018 - 09:30:03 PDT
