I have completed molecular dynamics simulation of some drug-DNA complexes, now I need to perform QM/MM calculations on the system. Please tell me as to how to set up a QM/MM calculation in gaussian software by ONIUM Scheme?
Please, consider the test jobs: http://www.cup.uni-muenchen.de/ch/compchem/testindex.html.
You can try to install ONIOM MacGyver using the below link:
https://github.com/eduardoftoliveira/oniomMacGyver
After you have done this, generate the topology and the coordinate files for the snapshot that you want to use for the ONIOM QM/MM calculation and use gau_prm2com command of the ONIOM MacGyver to convert both the generated topology and coordinate files to gaussian input file (.com). Thereafter, you will open the .com file using GaussView and partition your system into high layer and low layer. To do this, click on "Tools" follow by "select layer" on the GaussView menu.
NB: You will see a pdf document on how to use ONIOM MacGyver from the above link.
Full QM treatment is prohibitive for biomolecules. Try QM/MM and its variants.
Practical examples are a) setting the important region as QM region and others use MM Hamiltonians,,
b) try ONIOM, which may be more accurate but slower,
c) fragmentation QM/MM methods, which may be even more expensive but very accurate.
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