AMBER Archive (2005)

Subject: AMBER: Antechamber/Divcon assigned charges

From: Marc Christensen (mchrist551_at_hotmail.com)
Date: Thu Mar 03 2005 - 21:38:10 CST

I have a question regarding Antechamber and Divcon.

If one looks at the tutorial for simulating Sustiva using the General Amber
Force Field, the Divcon program is called to optimize the geometry then
assign Partial Mulliken, Partial CM1, and Partial CM2 charges (at least this
is what I gather from the Divcon.out file). However; when looking at the
charges that end up in the Sustiva.prepin file they are different from the
ones in the Divcon.out file.

For instance the charges on the chlorine from divcon.out

ATOMIC CHARGES:

   ATOM ELEMENTAL PARTIAL PARTIAL PARTIAL
    NO. SYMBOL MULLIKEN CM1 CM2
                     CHARGE CHARGE CHARGE

30 CL 0.00328 -0.02671 -0.02622

and the charge from the sustiva.prepin (-0.07512)

8 Cl1 cl E 7 5 4 1.742 119.676 -179.857 -0.07512

Sorry if this is a naļve question, but how are the charges that end up in
the prepin file being assigned - as a function of the ones calculated in
divcon or another source?

I have searched the reflector, DivconLite manual, and AMBER 8.0 manual to no
avail.

Thanks in advance…

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