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How to delete a solvent molecule close to a known coordinate

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Top 10 Contributor
21 Posts
Jana posted on 12-01-2008 5:24 PM

You can first define the distance and then use the delete command. Can anyone give a working example?

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Top 10 Contributor
14 Posts

Example:

1. !find the nearest solvent molecule around the known point

!say xpos, ypos and zpos are the coordinates of the known fixed point in space.

coor mindist sele point @xpos @ypos @zpos end sele segid SOLVENT end

2. !calculate the minimum distance between them.

!note: MIND should plus a small number, e.g. 0.0001, in order to avoid zero selection later,
!because of the different accuracy between the coor mindist calculation and ?MIND calculation.

calc distmin = ?MIND + 0.0001

3. ! make the deletion

delete atom  sele .byres. point @xpos @ypos @zpos cut @distmin .and. segid SOLVENT  end

 

 

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