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Jordy Homing Lam edited this page Oct 17, 2023 · 19 revisions

Welcome to the (Unofficial) Molsoft wiki!

Work SMART, work FAST, work SMILE. Work Molsoft!

ICM-Pro by Molsoft LLC is a very powerful tool in drug design and general structural bioinformatics. However, the documentation is vast and may take time to refer and master. Here, we provide a private unofficial outlook to a list of selected topics. A suggested reading sequence. Note that we are still shaping the Wiki, so please bare with us.

  • Resource for ICM Scripting
  • Basic I/O and Matrix Manipulations
  • Sampling of Conformations in ICM
  • Standard Workouts on Every SDF tables
  • Sanitisation of Molecules
  • Proteins, Nucleic Acids and Decorations
  • Analytical functions and Plots

CARC Access and CARC on demand

      • Connection to vpn off-campus. Use vpn.usc.edu
      • Connection to vpn in-campus. Use sslvpn.usc.edu. Instructions are similar to vpn.usc.edu, just change the address. 
    • Use Dashboard - CARC OnDemand (usc.edu) to avoid multiple trivial password typings + DUO, but both discovery1 and discovery2 may be assigned depending on the traffic in discovery1.

ICM Licensing

Flexible License in USC

You can download the ICM-Pro from Molsoft here. The ICM Flexible license is available on CARC (discovery1.usc.edu and endeavour.usc.edu) and your own PC.

      • Connection to vpn off-campus. Use vpn.usc.edu
      • Connection to vpn in-campus. Use sslvpn.usc.edu. Instructions are similar to vpn.usc.edu, just change the address. 
    • CARC. If you are using carc, login to the cluster; only discovery1 and endeavour were tested (previously it only works on these two). I would also recommend to use Dashboard - CARC OnDemand (usc.edu) to avoid multiple trivial password typings + DUO, but both discovery1 and discovery2 may be assigned depending on the traffic in discovery1.
    • Linux. In your .flexlmrc file it should contain the following line MOLSOFTD_LICENSE_FILE=@10.103.39.7. Put this at your ~/
    • Windows. Select Server when prompted for license. In the location field put @10.103.39.7

Node-locked License (for invited users only)

This is a license locked to specific computers using their MAC address. An explanation on MAC address as well as how to find it in different OS systems goes [here](https://www.cmu.edu/computing/services/endpoint/network-access/mac-address.html#:~:text=A%20MAC%20(Media%20Access%20Control,%2D63%2DC2%2D26.)! It only works if your computer is invited for registration, else skip this section as it will not work. When prompted for a license select the file and it's done.

FAQ

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