AMBER Archive (2003)

Subject: hydrogen bonding

From: seraphimo_at_gmx.de
Date: Tue Mar 18 2003 - 09:51:48 CST

hello amberians,
i did molecular dynamics of a macromolecule and a tip3 water under periodic
boundaries. the results yield that within a 3 angstrom sphere round the water
molecule there is no polymer segment. now i wonder about the hydrogen
bonding between water and macromolecule. in my understanding the water molecule
should be somehow closer to the surrounding polymer segments. i used gaff with
"hw" and "ow" atom types for the water. help will be appreciated.
best, mike. 

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