These are notes on how to install software, primarily for computational chemistry.
Just use conda, it will save you enormous amounts of time:
conda install -c rdkit rdkit
COSMO-RS on Linux
COSMO-RS is a fluid phase thermodynamics program. Usually, you use it from the GUI, COSMOthermX, but sometimes you need to run large numbers of calculations from on a server.
It's not immediately obvious how to install COSMOtherm (i.e., without the GUI) from the command line, so here's a step-by-step guide.
- Download COSMOtherm and, optionally, COSMObase (an add-on database with 12k+ extra molecules) from Biovia 3Dpassport download page. You should have a login from when you bought your license. I just installed the highest fidelity COSMObase files (TZVPD-FINE).
- Copy the zip files for COSMOtherm and COSMObase onto your linux server. For example, replace
USER@HOSTwith the username and address of your server and run the following command (removing the COSMObase file if you don't have it):
- Unzip the files on the server and copy the COSMObase files to the correct location if you have them. Replace 2020 with whatever version you have.
- Upload your license file to the server and copy it to the proper location:
- If you have any COSMObase files, you need to manually add them to the COSMOtherm XML configuration file:
- To use
cosmothermfrom the command line, make sure to add it to your path. You can modify
scp BIOVIA_2020.AM_BIOVIA_COSMOtherm_2020.zip BIOVIA_2020.COSMObase2020-BP-TZVPD-FINE.zip USER@HOST:/home
unzip BIOVIA_2020.AM_BIOVIA_COSMOtherm_2020.zip # If you have COSMObase: unzip BIOVIA_2020.COSMObase2020-BP-TZVPD-FINE.zip cp COSMObase2020 BIOVIA/COSMOtherm2020/COSMOtherm/DATABASE-COSMOIOVIA/COSMOt
mkdir -p BIOVIA/COSMOtherm2020/licensefiles/ cp license.txt BIOVIA/COSMOtherm2020/licensefiles/
# Open the configuration file (can do this alternatively with vi, nano, etc.) vim BIOVIA/COSMOtherm2020/config/settingsLinux.xml
Scroll down to the
<AllDatabases> tag, and add your database. For TZVPD-FINE, you need the following:
<Database> <DatabaseName selected="1">TZVPD-FINE-LARGE</DatabaseName> <DatabaseDirectory>../COSMOtherm/DATABASE-COSMO/COSMObase2020/BP-TZVPD-FINE</DatabaseDirectory> <parametrisation>TZVPD-FINE</parametrisation> </Database>
Then, under the
SQLiteSettings tag, add the database to the correct level, so COSMOtherm knows to look for it:
<DatabaseList parametrisation="TZVPD-FINE"> <DatabaseName>Default-TZVPD-FINE</DatabaseName> <DatabaseName>TZVPD-FINE-LARGE</DatabaseName> </DatabaseList>
This assumes the
BIOVIA directory is in your home directory. Put the reference anywhere you need it.
As an alternative to using the command line, you can request a copy of BIOVIA's COSMOpy library, which allows you to call COSMOtherm from python.