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
>>>
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>>
>
>
> --
> Tousif Hossen
> Research Scholar
> Department of Chemistry
> IIT GUWAHATI
> INDIA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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>
--
Tousif Hossen
Research Scholar
Department of Chemistry
IIT GUWAHATI
INDIA
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Received on Sun May 06 2018 - 23:00:01 PDT
