AMBER Archive (2007)

Subject: Re: AMBER: Problem with Getting SHAKE to work

From: David A. Case (case_at_scripps.edu)
Date: Mon Sep 17 2007 - 11:38:26 CDT

On Sun, Sep 16, 2007, David Cerutti wrote:

>
> Fixing this, however, does not do much. Like I said earlier, however,
> SHAKE does seem to work on the protein atoms

Sander or pmemd reports a line like this:

Number of triangulated 3-point waters found: 11324

Are you getting this printout, with the proper number of water molecules?

Water SHAKE is done in the routine setlep() [called shake_fastwater() in
pmemd.] You might put some print statements in there to see what parameters
this is being called with.

Can you make a small system that shows this problem? It's hard to debug just
based on the information we have so far.

....dac

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