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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Received on Wed May 11 2011 - 10:30:04 PDT
