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
>
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Received on Fri May 04 2018 - 21:30:03 PDT
