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
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Received on Sun May 06 2018 - 07:30:03 PDT
