National University of Singapore

Discovery Studio, a comprehensive suite of modeling and simulation solutions for protein modeling and computational chemistry from Accelrys Inc, includes a diverse collection of sophisticated software applications and provides advanced software solutions for life science researchers.

License:

At Computer Centre, licenses for the following Discovery Studio modules are available. Please take note the terms and conditions in the academic license and service agreement we have signed with Accelrys. Your download and usage of the software implies your acceptance/compliance.

   Visualizer
   Biopolymer
   CFF
   Charmm
   Analyzer

To install Pipeline Pilot and Discovery Studio 3.5 Client on your Windows PC:

• If you have any DiscoveryStudio version older than 3.5 on your PC, please go to Control Panel -> Add or Remove Programs, Remove DiscoveryStudio 3.1 and Pipeline Pilot Sever 85. You'll be asked to stop scitegic_apache service while the software are removed, click Yes to proceed.
• Go to http://bobcat.nus.edu.sg/DS21windows/DS3.5, download the specific files onto your local harddisk:
  
  • Download PP85_with_CU3_Win32.zip and DSCollection_new.lic if you are running 32-bit Windows OS. Extract the files and go to the bin folder, double click scitegicsetup.exe to install Pipeline Pilot Server 8.5 and Discovery Studio client 3.5.
    
  • Download PP85_with_CU3_Win64.zip and DSCollection_new.lic if you are running 64-bit Windows OS. Extract the files and go to the bin folder, double click scitegicsetup.exe to install Pipeline Pilot Server 8.5 and Discovery Studio client 3.5.
    
  • Download DS35Client.exe if you only want to install Discovery Studio client 3.5 on your Windows PC, with which you can only build models and view simulation results but not run any jobs.
    
  • Download DS35Client.tgz if you want to install Discovery Studio client 3.5 on your Linux servers.
• Starting from Discovery Studio 3.1, Discovery Studio is placed under Pipeline Pilot, the Accelrys’ scientific informatics platform. Click and download this Piperline Pilot license and keep it in your local harddisk, choose this file when you are asked for the license of Piperline Pilot at the initial stage of installation. This license allow you to use the basic modules of Piperline Pilot even after the expiry date indicated in the license file.

Getting License from the License Server "lion4" "lion2" and "lion3"

• After you install Piperline Pilot on your PC, start the License Administrator 7.6.8 from Accelrys --> Licensing, click License Server --> Connection --> Edit... --> Add "lion4" "lion2" and "lion3" (or the IP addresses shown below) as the hostnames (check the "Redundant Servers" box) and keep the default 1715 as the port number and click OK to exit. You'll see a "started" as the status of the license server connection.
• For Windows Vista and Windows 7 users, you when you start the License Administrator 7.6.8, you need to right click on the License Administrator 7.6.8 button and choose "Run as administrator".
• Before this, you may want to modify your "hosts" file on your PC to add this line under the line "172.0.0.1 localhost":
  
  172.18.173.56 lion4.nus.edu.sg lion4
  172.18.165.5 lion2.nus.edu.sg lion2
  172.18.165.160 lion3.nus.edu.sg lion3
  
  

The "hosts" file can be found at C:\WINDOWS\system32\drivers\etc.

Run Small Jobs on Your Local PC or the Pipeline Pilot Server:

Run your small jobs on your local PC or on the Pipeline Pilot server: after you start Discovery Studio 3.5, click on File -> Change Server, type localhost as the Server name if you have installed Pipeline Pilot server on your PC, or type 172.25.192.16 as the Server name. When prompted for userid and password, key in your NUSNET userid and password to connect to the server.

For jobs which need to run for a long time and need large memory, you should follow the instruction below to submit them to the LSF batch queues.

Prepare and submit large CHARMm Jobs to the LSF Batch Queue:

• Before you run your simulation, make these two settings on Preferences under Edit menu:
  • Click on Files Explores, Put in a local path in the "Select path for default folder".
  • Click on Protocols, tick "Save Intermediate files when running protocols" option.
• Set the number of the steps to a small number (e.g. 10) and run the job. Once the job is done, the Intermediate files will be saved in your "default folder"
• Transfer the files to your subfolder under /hpctmp. Modify the path in the RunCHARMm.sh file and the number of steps (NSTEP) in the minimization.inp file and submit CHARMm jobs using LSF commands:
  
  > bsub -q linux64 -m atlas5cluster -o my_job.eo ./RunCHARMm.sh
  > bsub -q atlas5_large -o my_job.eo ./RunCHARMm.sh
  
  

Help

Discovery Studio on-line help and tutorials are available by clicking on the Help button on the Discovery Studio Client Interface. If you have any problems or queries, please send emails to ccehpc@nus.edu.sg