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
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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
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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
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>
--
Tousif Hossen
Research Scholar
Department of Chemistry
IIT GUWAHATI
INDIA
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 07 2018 - 08:30:02 PDT
