Thanks Marek for suggestion its working.
But still I am in cofusion that if closest command not using distance criteria
for slection of water molcules then how it selcts water molecules around given
mask atom?
> Hello Sangita,
>
> I solved recently the same problem (however with different molecules).
>
> From information which you wrote I would suggest you this approach:
>
> ---------------------------------------------
> strip :Na+ (or/and Cl-)
> solvent byres :WAT
> closestwater 10 [DNA MASK] first noimage
> closestwater 5 [PROTEIN MASK] first noimage
> --------------------------------------------
>
> This command sequence should strip Na+/Cl- ions (If you have some in box),
> then 10 closest waters
> to DNA will be selected and the last command will select from that 10
> waters just 5 closest to your protein so with high probability you select
> by this approach
> just water molecules involved into DNA/proteinbinding.
>
>
> Before that above commands it is of course a good idea to reimage your
> trajectory, so
> that the center of mass of your system (DNA/PROTEIN) is in the center of
> the box.
>
> Something like this:
>
> -----------------
> center [DNA/protein mask]
> image familiar
> -----------------
>
> (check command "image" in Amber manual)
>
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
> Dne Wed, 11 May 2011 19:29:30 +0200 Sangita Kachhap
> <sangita.imtech.res.in> napsal/-a:
>
>> Hello All
>>
>> I have to do thermodynamic analysis of water mediated H-Bond using MMPBSA
>> for this I have processed trajectory using closest command to keep 10
>> water
>> molecules.
>> When I visualized the processed trajectry 5 out of 10 are involve in
>> water
>> mediated H-Bond between protein and DNA and some are too far.
>>
>> When I cheked the mailing list there is some discussion about closest
>> command
>> that it not
>> use any distance criteria to select closest water molecule around mask
>> atom.
>>
>> According to above discusion if I gives command closet 10 mask atom it
>> will select
>> 10 water molecule even if 10th water molceule is 100 angostrom away from
>> the
>> mask atom.
>>
>> Here I want to know that how it chose which water molecule sholud be
>> keep or not
>> since there are too many water and some of the water are morenear to
>> 10th water
>> that is select even it is 100 angostrom away from mask atom.
>>
>> Is closest command selects water molecule from the starting number of
>> water
>> molecule in the prmtop?
>>
>>
>> With regard
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 6114
>> (20110511) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>>
>>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed May 11 2011 - 23:30:02 PDT
