AMBER: sander.QMMM: CHARGE keyword in file

From: M. L. Dodson <>
Date: Wed, 04 Aug 2004 14:23:29 -0500

Hi ambers,

A question about sander.QMMM (AMBER8) input.

I was doing a preliminary minimization run with a structure that
had Na+ added to neutralize the charges on DNA (whole system
charge = 0). The QM atoms summed to neutrality, as well, so I put
CHARGE=0 in the file. This run completed without error.
I repeated the run after adding a phosphate group to the QM atoms,
so I changed to CHARGE=-1, but the run immediately crashed with
the error message that I had an odd number of electrons in a
closed shell calculation.

So the question is: Does CHARGE in the file mean the
charge on just the QM atoms? Or on the whole system? My result
indicates the whole system, unless I am doing something else
wrong, which is what I'm really worried about. (Details to anyone
who needs them, but I'll not bother the whole list.)


Bud Dodson
M. L. Dodson                      
409-772-2178                                FAX: 409-747-8608
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 04 2004 - 21:53:00 PDT
Custom Search