> 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
>>>>
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>>>>
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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%7C704d822c358a47849a1649e20b75f941%7C0%7C1%7C636611850747339865&sdata=1gJjfWNBgGO4OsgT1dY%2FCsXeuuAvLTAgOo70BxBOf3c%3D&reserved=0
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Tousif Hossen
> Research Scholar
> Department of Chemistry
> IIT GUWAHATI
> INDIA
>
--
Tousif Hossen
Research Scholar
Department of Chemistry
IIT GUWAHATI
INDIA
_______________________________________________
AMBER mailing list
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Received on Mon May 07 2018 - 07:00:03 PDT
