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.
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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- application/octet-stream attachment: QMMM.zip
Received on Thu Nov 14 2019 - 07:00:01 PST
