Schrödinger

If you have corrections or general tips regarding this documentation, please contact us at support@c3se.chalmers.se

Changing Schrodingers temporary working directory

It is recommended to use your $TMPDIR for Schrodingers temporary working directory instead of the default one. Do this by adding -TMPDIR $TMPDIR to your jobscript.

For example:

ligprep -inp <inputfile> -HOST localhost:20 -WAIT -TMPDIR $TMPDIR

Known errors

If your job has previously crashed you might get an error message when trying to run Schrodinger which ends with EOFError: EOF when reading a line.

You can remedy this by adding -OVERWRITE to your jobscript.

For example:

ligprep -inp <inputfile> -HOST localhost:20 -WAIT -TMPDIR $TMPDIR -OVERWRITE

License

You must specify the license in the file ~/.schrodinger_license If you need to use the Chalmers license server, you should specify

SERVER schrod1.lic.chalmers.se ANY 27040
SERVER schrod2.lic.chalmers.se ANY 27040
SERVER schrod3.lic.chalmers.se ANY 27040
USE_SERVER

however, your user must be registered on Chalmers license server else you will only get license errors. You must contact Leif Eriksson leif.eriksson@chem.gu.se and approve the license cost. C3SE does not own or manage any Schrödinger license, and can not help you beyond this information.