AMBER Archive (2007)

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

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Mon Sep 17 2007 - 15:36:59 CDT

For the time being, I ahve resolved this issue. The problem was two-fold
and hence harder to pin down. First, I had forgotten to "AddAtomType" one
of the new hydrogen atom types I had defined. Second, I had forgotten,
sometime in the last two days, that the bellymask describes the atoms you
don't want frozen, not the other way around. Taking care of these has put
my bond lengths back on track. I am still getting some pmemd crashes
after vlimit errors, but this is probably because I'm running roughshod
over minimization protocols at the moment while I explore the best way to
pack solvent around a funny system.

Dave

On Mon, 17 Sep 2007, David A. Case wrote:

> 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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