AMBER: ptraj average structure strip water

From: Youyi Peng <pengyo.UMDNJ.EDU>
Date: Fri, 02 Mar 2007 14:52:02 -0500

I did a molecular dynamics simulation for a solvated system. Hydrogen
bonds between solvent water and the ligand were found by ptraj/hbond.
But I don't know the water IDs. I want to keep these water molecules
hbonding to the ligand in the average structure but strip out other
water molecules. Is this mission possilbe? If yes, how to do it?
Any suggestion is highly appreciated.

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Received on Sun Mar 04 2007 - 06:07:58 PST
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