Hi Kriti,
You can define your own basis sets. The basis set is in directory $QUICK_BASIS, which will be defined after you source amber.sh.
You can create a new custom basis set file (e.g. “CUSTOM.BAS") into which you copy the desired basis set information for each element. You can get the basis set information from the existing basis set files in directory $QUICK_BASIS. You will have to add the basis set name to the file "basis_link". I recommend to also copy the corresponding SAD guess information for each element (e.g. into directory “CUSTOM.SAD").
If you do not have write permission to the AmberTools installation directory, then you can use a different directory. In this case you will have to point QUICK_BASIS to the desired directory, e.g. `export QUICK_BASIS=~/my_basis_sets`.
Information on how to add new basis sets is also available in the online documentation at
https://quick-docs.readthedocs.io/en/latest/developer-guide.html#adding-new-basis-sets
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On May 20, 2024, at 7:57 AM, Kriti Shukla via AMBER <amber.ambermd.org> wrote:
Respected Community,
I am trying to set up the QM/MM environment in my system using Quick with
Amber, which is an enzyme with Zn in its active site. But in assigning the
basis set, I need two types of basis sets: one for the protein residues and
one for the metal.How to do so and also how to treat the water molecules
surrounding them as they are interacting with both type of species. Your
Guidance will be very helpful.
thanks and regards
Kriti Shukla
Research Scholar
Department of Chemistry
Indian Institute of Technology, Kharagpur
India. 721302
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Received on Mon May 20 2024 - 14:00:02 PDT
