[AMBER] There is an bug in how Amber preserves charge neutrality in QM/MM system when ORCA is the targeted QM tool.

From: James Kress <jimkress_58.kressworks.org>
Date: Sat, 16 Nov 2019 11:08:40 -0500

I am trying to set up a single point QM/MM calculation on a single frame
extracted from a charge neutralized MD run using Amber18 with AmberTools 17.
I use the following command line to create the QM and MM selections:

sander -O -i sample.in -o sample.out -p baseline_salt.prmtop -c
baseline_salt_wrapped_fr1000.rst7 -r sample.rst

The sander input file is quite simple and is attached along with every other
relevant file in the archive QMMM.zip to the limit imposed by the mailing
list. If anyone is interested in eliminating this bug (or showing me what I
did wrong) I can send the prmtop and baseline_salt_wrapped_fr1000.rst7 files

The problem I have is that the QM region has a -18 charge (as can be seen
from an examination of the pdb file). However, the MM region has a +36.11
charge (as can be seen from an examination of the old.ptchrg.xyz file).

What have I not properly specified in order to ensure I have a charge
neutral system?

Thanks for any help you can provide.

Jim Kress

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Received on Sat Nov 16 2019 - 08:30:02 PST
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