AMBER Archive (2008)

Subject: Re: AMBER: Clarification re qmmask

From: Gustavo Seabra (
Date: Thu Oct 16 2008 - 13:22:41 CDT

I just made some tests and I can confirm the problem. However, it does
not come from the qmmask, which, as Ross pointed out, only uses a
general Amber routine to choose the atoms.

Apparently the problem comes from the atommask routine that is not
dealing with the distance parameter correctly. Basically, if you
include this operator, it returns *ALL* atoms as being found by the
mask. Thus, you get a QM region that includes ALL the atoms.

The message you are getting from sander_bomb is correct: In the end,
you are attempting a calculation with a periodic cell that includes
all the atoms, which is not allowed by the current implementation of


On Thu, Oct 16, 2008 at 1:24 PM, Benjamin Roberts <> wrote:
> Hi all,
> I seem to have discovered that the qmmask doesn't like a selection specified
> via the "<:distance" mask parameter (e.g., ':1 <:5' for residues within 5
> angstroms of residue 1). In such cases, Sander bombs out (quite literally:
> "SANDER BOMB" is received), informing me that the periodic cell is too
> small. I get this response even if I reduce the distance to 0.01 (thus
> ensuring that absolutely nothing outside residue 1 itself is included in the
> QM/MM mask). On the other hand, if the mask given is :1 only, or even if
> residues near :1 are explicitly included in the mask using their own
> numbers, this problem is not encountered.
> Is this deliberate, and if so, is the rationale behind it known? It's
> certainly not something I could have guessed from the manual, which says,
> "see mask documentation for more info" (p. 93), implying, "just observe one
> of the mask formats and all will be well".
> I could understand this if periodic attempts to rebuild the QM region from
> the mask take place, thus tampering with energy conservation. On the other
> hand, I would have expected (not having seen for myself, admittedly) that
> the QM region gets built only once, at the start of the simulation. Is this
> rebuild going on, or is there some other cause?
> Ben
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