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Jordy Homing Lam edited this page Mar 13, 2025 · 22 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 [email protected]. 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.

Remark on Installation

After it is installed it prints the following message; read each line and follow the instructions from there.

------------------------------------------------------------------------------------
The package icm-3.9-3a installed.
------------------------------------------------------------------------------------

/tmp/selfgz17554
Set environment variable by adding the following lines to your ~/.cshrc file
  setenv ICMHOME "/home/nazarova/icm-3.9-3a//"
or
  set ICMHOME="/home/nazarova/icm-3.9-3a//"; export ICMHOME;
depending on your shell

****************  A T T E N T I O N  ******************
  PRODUCTS  ICM-Browser-Pro,  ICM-Bio  and ICM-Pro
  REQUIRE A COMMERCIAL LICENSE KEY. TO GET THE KEY SEND
  TWO LINES BELOW TO [[email protected]](mailto:[email protected])
 

"Spacibo no niet spacibo" is your hostid.
# ICM version 3.9-3a/Lin-iX86-64bit/g6.5/Release/HardwareGL/Gui263940/WebKit/Cuda/Video/FlexLM/LMX/OpenMP/SSE2. Nov  8 2022 19:04.
# Email the previous line to [[email protected]](mailto:[email protected]),
# ask for a license and store it in the 'license.dat' file

3910867215 is your molcart hostid

  save your license obtained from Molsoft LLC into the
  file /home/nazarova/icm-3.9-3a//license.dat.

  1. set up the system variable $MOLSOFTD_LICENSE_FILE
  with the command
    setenv MOLSOFTD_LICENSE_FILE /home/nazarova/icm-3.9-3a//license.dat
  or
    set MOLSOFTD_LICENSE_FILE=/home/nazarova/icm-3.9-3a//license.dat;
    export MOLSOFTD_LICENSE_FILE;
  depending on your shell.

  2. make sure you specified it correctly.
     e.g. cat $MOLSOFTD_LICENSE_FILE

  3. set permissions so that everyone can read the file
     e.g. chmod a+r $MOLSOFTD_LICENSE_FILE

  If you have problems with installation take a look to
  the installation instructions at
  [www.molsoft.com/support](https://urldefense.com/v3/__http://www.molsoft.com/support__;!!LIr3w8kk_Xxm!qzaC8AIbTNiMyZV-fqteMlbRcucUkXWr-10dOxCfCWrsAoP-K6Zoe3pz3BkYV45CDZKbYb0_HD3bEhyW9Q$) another one time.  Check our
  FAQ at [www.molsoft.com/support](https://urldefense.com/v3/__http://www.molsoft.com/support__;!!LIr3w8kk_Xxm!qzaC8AIbTNiMyZV-fqteMlbRcucUkXWr-10dOxCfCWrsAoP-K6Zoe3pz3BkYV45CDZKbYb0_HD3bEhyW9Q$) if somebody already
  had the same problem.  Also your questions or
  suggestions are welcome at [[email protected]](mailto:[email protected])

  To start ICM type in your terminal:
   
    /home/nazarova/icm-3.9-3a//icm -g

  or (for 64 bit system)

    /home/nazarova/icm-3.9-3a//icm64 -g

FAQ

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