AMBER Archive (2009)

Subject: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins

From: sychen (u8613020_at_msg.ndhu.edu.tw)
Date: Tue Apr 14 2009 - 11:33:03 CDT

Dear all,

I'm a beginner for using qm/mm md in AMBER, and I got a question as follows,

Is the qmcharge for one GLU and one ASP residue involved in the qm
region to be -2, while all the other residues in the mm region?
I found that the part of output indicated that it was -1.637
Although the calculation done without errors, I'm wondering if such adjusting is ok?

###part of the output as below
QMMM: ADJUSTING CHARGES
QMMM: ----------------------------------------------------------------------
QMMM: adjust_q = 2
QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge.
QMMM: qm_charge = -2
QMMM: QM atom RESP charge sum (inc MM link) = -1.637
QMMM: Adjusting each MM atom resp charge by = 0.000
QMMM: Sum of MM + QM region is now = 0.000
QMMM: ----------------------------------------------------------------------

Thank you!

Sincerely,
yuann

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