Specifying QM/MM system

ilya ily... at gmail.com
Thu Oct 9 12:43:53 UTC 2008

Hi all !!

I try to make a QM/MM sim of a small molecule (QM part) in a water box
(MM part). And i have several questions.
1. When the program generates connectivity (CONN_FILE_FORMAT GENERATE)
it also generates connectivity for QM subsystem and asks for bond/
torsion params, which are not needed for QM part as it is described
with DFT. So should i specify QM part as ISOLATED_ATOMS to get rid of
2. Even when i use ISOLATED_ATOMS on QM subsys it steel needs charges.
Do i need to specify them (maybe they are needed for computing
nonbonded interface QM/MM forces/energies?) or do something else?

Thanks in advance.


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