Software Name: MOLECULAR OPERATING ENVIRONMENT (MOE)

[andreaalfarochacon-afk]

Requestor Last Name

Alfaro Chacon

Research Group

Wohlfert

Additional Interest

No response

Application Information

Dear CCR Support Team,

I am writing to request the installation of Molecular Operating Environment (MOE), developed by Chemical Computing Group, on the CCR cluster.

1. Benefit to multiple groups
   MOE is widely used in computational chemistry, structural biology, and drug discovery. At UB, multiple groups such as Structural biology, Microbiology & Immunology, Pharmacology & Toxicology, Chemistry could benefit from access to MOE for molecular modeling, docking, and computational simulations. MOE is a great software to do protein-protein interaction proteins that are more complex than simple molecules.

2. Actively supported software
   MOE is an actively maintained commercial software with regular updates, bug fixes, and security patches. The developer provides full technical support and documentation (https://www.chemcomp.com/en/Products.htm
   ).

3. Licensing considerations
   We understand CCR’s policy that software must be open source or free for academic use. MOE is commercial and requires an academic site license. I am currently checking whether UB already has such a license or if an academic license could be purchased and integrated with CCR. Please advise if CCR could host the software under an institutional license.

4. Technical compatibility
   MOE runs on Linux and is designed to work in HPC environments (“Laptop – Cluster – Cloud – Pipeline” deployment modes). It allows flexible installation paths, which should be compatible with CCR’s software environment.

5. Non-GUI usage
   While MOE has a powerful GUI, many workflows (e.g., molecular docking, QSAR modeling, simulations) can be executed in batch mode through the scripting language (SVL) and command-line tools. This makes it feasible to run non-GUI jobs through the CCR queueing system.

6. No persistent services required
   MOE does not require perpetual background services or databases. It can be run as a stand-alone application or via scripts submitted to the cluster.

https://www.chemcomp.com/en/Products.htm

Version

NA

Software Release Version

No preference

Additional information

No response

[dsajdak]

Hi @andreaalfarochacon-afk Thank you for your detailed information and for reading through our software policy before requesting this software. I can find no instructions for installing these packages so it's difficult for me to say whether or not they can be supported on our systems. In general, it can be difficult to support commercial packages because of library linking issues we encounter when installing them. However, it appears you can request an evaluation of the software so you could try it out on our systems. It would not be something we would install globally however. You would need to install this in your research group's private project directory so that you're the only group that gets access to the license. In order to use a licensed software on our systems, it must be a floating license, not a node locked license. We don't support license servers, but sometimes departments will support them and we can allow the connection to happen outside of CCR to your department's server.

[dsajdak]

If the vendor provides Docker or Apptainer containers for their software, this would be the ideal way to use their products on our systems.

[andreaalfarochacon-afk]

Hi Dori Sajdak,

Thanks for the guidance. I’ve contacted Chemical Computing Group (info@chemcomp.com) to confirm: whether MOE is available as a Docker/Apptainer (Singularity) container, and whether they can provide a floating license (not node-locked).

If they confirm container availability, I’ll plan to install/run MOE within our group’s private project directory (not globally). A couple of quick questions on the CCR side so I’m ready once they reply:

1. Apptainer best practice: Do you prefer I bring a prebuilt .sif (converted from Docker) vs. pulling and building on-cluster? Any limits on image size or recommended storage path (e.g., /projects/[group]/containers/)?

2. License connectivity: If our department hosts a MOE license server, are there specific port/hostname details you would need from us to allow outbound connections from CCR compute nodes?

3. GUI vs. headless: If we need any MOE GUI features, what’s CCR’s recommended approach (e.g., X11 forwarding or no-GUI/headless only)?

4. Evaluation workflow: If CCG offers an evaluation license, is there anything special I should provide to you (e.g., license file path, environment variables) to streamline testing?

I’ll update you as soon as I hear back from the vendor. Thanks again for your help.

Best,
Andrea

[andreaalfarochacon-afk]

If the vendor provides Docker or Apptainer containers for their software, this would be the ideal way to use their products on our systems.

Dear CCR Team,

I contacted the vendor (Chemical Computing Group) regarding the Molecular Operating Environment (MOE) software. They confirmed that MOE does not provide official Docker or Apptainer containers. However, they do provide a tutorial and instructions for users to create their own containerized environment if needed.

In other words, while there isn’t a prebuilt container available from the vendor, the software can be containerized by the user following the vendor’s guide.

Please let me know if this setup would be acceptable for installation on the CCR systems.

[dsajdak]

It's acceptable to try it but there are no guarantees. I would ask for a trial license and to see the instructions for building the container. For the rest of your questions:

1. Most containers can be built on our systems but occasionally elevated privileges are required and the build will fail. I can't say if that will happen in your case, especially without seeing the instructions. But usually what we say is, give it a try on our systems and you can also install apptainer on your PC and build it, if necessary. See here for more container info.
2. We don't need to explicitly allow outbound connections. However, you will need the license server hostname and port to point the application to when it runs.
3. We don't allow X11 forwarding. The container would have to have the X11 libraries installed and be able to run without additional software installed on the compute nodes.
4. This is also hard to say - sometimes a company will provide a license file that can be used on our systems without additional setup. Sometimes the software will require a license server to be setup, even for testing.
   Once you get a trial, if you want to open a ticket with us we can look further into the instructions they provide and see if we can give you any guidance to get it running.