Also if it's showing water outside the cavity, it means either your mask is badly chosen, or that there's not actually water in your cavity. Watershell will give you a better idea on both those, since it searches based on distance criteria around a given 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
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Received on Sun May 06 2018 - 08:00:02 PDT
