Dear AMBER
In my MD simulation, there are two water molecules forming a bridge between the ligand and the receptor.
I used closestwater command in ptraj to keep the closest two water molecules into two atoms of the ligand
trajin MD.mdcrd
strip :Cl-
closestwater 2 .830,.834 oxygen
trajout WATMD.mdcrd
the problem was that I wanted to keep only one water molecule closest to each atom of 830 and 834 of the ligand. In some snapshots, I found the two water molecules were on the same atom (e.eg. .830).
How can I overcome this issue?
What the appropriate command can be used to keep only one closest water molecule to each atom?
Thanks in advance
W. Flak
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Received on Sat Oct 09 2010 - 09:00:03 PDT
