Thanks David, that helps a lot. I've studied define_frames() some more, it appears to me the rules are as follows:
1. For four site water, the extra point always lies along the axis of the molecule, and the distance from the oxygen is determined by the length of the bond.
2. For five site water, the extra points lie above and below the central axis, again at a distance set by the bond length. The angle they make with the H-O-H plane is hardcoded as 54.735 degrees, which corresponds to TIP5P.
If those are correct, I think I'm all set.
One other question: is it safe to assume that water molecules will always be called "WAT" in prmptop files?
Peter
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Received on Mon Feb 13 2012 - 16:00:02 PST
