AMBER: Clarification re qmmask

From: Benjamin Roberts <>
Date: Thu, 16 Oct 2008 13:24:45 -0400

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?


Benjamin P. Roberts
Postdoctoral Research Associate
Quantum Theory Project
University of Florida
2301 New Physics Building #92
PO Box 118435
Gainesville FL 32611-8435
Phone: +1 352 392 6712
Cell:  +1 352 222 3677
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Received on Fri Oct 17 2008 - 05:11:33 PDT
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