Re: [AMBER] angles and dihedrals for lone pairs

From: case <>
Date: Tue, 7 Aug 2012 21:52:12 -0400

On Tue, Aug 07, 2012, Ivanov, Maxim wrote:
> According to the code EP around oxygen in TIP5P has to be in tetrahedral
> sites with angle between two EP equal 54.735*2=109.470. And this angle
> has to be fixed.
> However, minimization of TIP5P give values around 109.5 degrees
> depending on number of steps. What is the reason for this?

Here's what I think is happening, but I don't have time right now to make
sure: At each step, the code calculates the positions of the EP's based on
the coordinates of the heavy atoms. It then moves all atoms and applies SHAKE
constraints to the hydrogens (but not to the EP's, since that is not
necessary). At this point, the geometry of the EP's is not in sync with the
heavy atoms (that will be done during the next energy evaluation), but the
coordinates may get dumped to the output anyway.

This is arguably a bug: the code could readjust the coordinates of the EP's
prior to printing out their coordinates. Bottom line is, unlike what I said
before, that you may not be able to trust the coordinates of the EP's in the
output file. (In one sense, they should not even be there: the coordinates of
the EP's are not independent variables, but are always determiend from
positions of the "real" atoms.)

As I said, I'm not sure this analysis is correct, but I don't have any
opportunity right now to study the code to make sure.


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Received on Tue Aug 07 2012 - 19:00:04 PDT
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