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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>
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>
>
>
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Received on Wed May 11 2011 - 11:30:02 PDT
