Introduction to Molecular Modeling in Drug Discovery Online Course

I have registered with a start date in the future.

When will I get more information about how to access the course?

After completing your registration, you should have received an email with the subject line “Introduction to Molecular Modeling in Drug Discovery – Welcome and Confirmation of Enrollment” that has some information about your registration. Additionally, at 10:00 AM ET on the day that your course is set to open you will receive an additional email with the subject line “Introduction to Molecular Modeling in Drug Discovery — Welcome and Credentials!” with everything you will need to get started with the course. If you have not received either of those emails please make sure to first check your Spam and Junk folders and let us know so we can find other ways to deliver the information.

How can I change my course start date?

You can still change your course start date after registering for a course. Please let us know as soon as possible and specify your desired new start date

I am currently taking the course.

How do I access the course page?

You can access the course page by going to That site is only for accessing the course content. Your username for the course page will be your email, and your temporary password will be shared in an email with the subject line “Introduction to Molecular Modeling in Drug Discovery — Welcome and Credentials!

To register for another course go to, find your desired course, and register there.

How do I access the virtual cluster (i.e. how do I access Maestro and LiveDesign)?

Your credentials for the virtual cluster that you will use to access web-based Maestro were shared in an email with the subject line “Introduction to Molecular Modeling in Drug Discovery — Welcome and Credentials!”. If you have not received that email please make sure to first check your Spam and Junk folders and let us know so we can find other ways to deliver the information. Your username with the Maestro virtual workstation will be a user number, for instance “user5”.

To access the virtual cluster, choose the geographic region that is closest to you:

North America/South America access
Europe/Africa/Asia/Australia access

Please be aware that Maestro is not the same as Maestro Elements. Ensure that you open Maestro for your work within the course.

Your LiveDesign username will also be a user number, for instance “user5”.
Global LiveDesign access:

Please note that each Schrödinger Online Course has a different set of virtual cluster URLs. If you have enrolled in multiple courses please be sure to use the correct course-specific URL to log into the virtual workstation for the course you are currently working on. The virtual clusters require high-speed internet for ideal performance.

Please also remember that uploading or downloading files or data to web-based Maestro that are not related to the course is strictly prohibited.

If I have my own version of the Schrödinger software suite, can I use this instead of the virtual cluster access?

The virtual cluster comes equipped with all of the files and licenses needed for working through the course, and conveniently we have the ability to troubleshoot in your instance if you run into any issues. However, you are welcome to use your local installation of Maestro if you choose! You can download the course project files here.

Please note that this is a rather large file download and may take a few minutes depending on your internet speed. The course uses the 2022-4 version of the software. If you are using a different version, your screen may not match the videos.

Can I work on the course on the weekend and over the holidays?

Yes! We encourage you to take your time when working on weekends or over the holidays. As our online course support team works 9am-5pm ET working hours and observes US holidays you may notice a delay in grading or email responses when the company is closed. Rest assured we will take the time to review your queries and grade your submissions when we return to the office. We work to ensure the course sessions take into account these delays when choosing start and end dates.

I only have one screen, so it’s tricky to watch videos and follow along. What can I do?

If you have an additional monitor, we’d recommend using both. If you are limited to one screen, you can try printing out the downloadable material and using that to guide you. Also, feel free to pause videos at any point to catch up on web-based Maestro or LiveDesign.

Can I skip over course content and still finish the course?

Technically, yes, you are welcome to bounce around to complete the modules most relevant to you. Completion of the course is determined by the certified completion of the final case study assignment. However, to receive the full benefit of the course, we recommend that you complete all of the components of each module.

Why is web-based Maestro slow? When I rotate structures, my screen is jumpy

The usability of web-based Maestro is dependent upon the available internet speed. Access to a computer with a high-speed internet connection (8 Mbps or better) is recommended. You can check your internet speed here.

My Maestro jobs are taking a while to complete. What should I do?

There are two different hosts that you could use to run jobs in the Maestro instance that we are hosting – localhost, and compute(40) or cpu(64). The default host is localhost, and we recommend using it for any calculation that is expected to take fewer than 2 minutes. For any calculation that we anticipate will take more than 2 minutes, we recommend using the compute(40) or cpu(64) host (and have indicated that explicitly in the instructions). It may take a few minutes to spin up the node when you are using it for the first time, so please be patient. To change your host, click the cog next to the Job name, and click the dropdown next to the CPU host to choose compute(40) or cpu(64) depending on the instance you are on.

I’m getting an error every time I try to save a file, or run a job that leads to a pop-up that says “An error has occurred”

The root of your issue is very likely that your Working Directory is set to a directory that you do not have ‘write access’ to – in this case it would be the course-data folder. If you change your working directory to a different folder (such as the Course folder on your Desktop) you will no longer see these issues.

I can’t find the file/project file that I’m looking for

Make sure that you’re looking in the correct place for the specific file type you are looking for. For Project files, make sure to go to File > Open Project — when you do that you will not be able to see regular structure files (though they can still be present in your directory). For structure files, make sure to go to File > Import Structure.

I don’t have a Job Server

Please note that your local instance of Maestro may have a Job Server or Job Monitor. The functionality is very similar for each. The Job Server allows calculations to be run on remote compute resources while you are away from the workstation.

I cannot find and open Ligand_Designer.prjzip

In Maestro, navigate to the upper left corner and choose File > Change Working Directory. Select the Course-data folder on your Desktop as your Working Directory. Next, go to File > Open Project and choose Ligand_Designer.prjzip

The pH is noted as N.N. instead of 7.4

This is a known issue that has since been corrected in more recent releases of Maestro. Manually toggling or editing the pH in the Global Settings menu at the top of the Protein Preparation Workflow panel will correct the issue you are seeing and your chosen pH will be displayed where you are currently seeing N.N.

I have a different number of LigPrep output entries in the Entry List

Additional LigPrep output structures are due to improvements in the software and/or changes to the default settings in new releases. Please double check your calculation input and proceed as usual with your output.

I have submitted my assignment and am waiting for grading

Schrödinger Education Team members are based in the US, so grading of assignments may have a delay depending on when they are submitted. In general, we strive to have a quick response during regular business hours and will do the best we can during our evenings. Please do not expect a response over the weekend. The end of the course can get a bit busier than normal as it’s essentially “crunch time” for many participants. We appreciate your patience here. We will be sure to provide you with assignment feedback with enough time to resubmit to earn a course certificate.

How do I log out of the Maestro Virtual Workstation?

When done working in the virtual cluster, close down all of the open windows and logout. For Mac users, press SHIFT + CTRL + CMD and for Windows users, press SHIFT + CTRL + WINDOWS/START KEY. A panel appears on the left side of the screen. Click on your username at the top-right corner and click logout

When I try to open my Maestro project I get a message saying “The requested project is currently in use by another Maestro session…

This message arises when the Maestro session was not closed before logging off the virtual cluster. Click “Yes” to proceed. For best practices, please make sure you close Maestro before logging off the virtual cluster.

Can I have an extension?

The timing of this course has been found to work well with the schedule of a participant with a full-time role. However, we understand that schedules are dynamic and we would like to ensure all participants feel they have adequate time to complete the course modules and final assignment. Due to the nature of the computational resources that are provisioned for the course, extensions are evaluated on a case-by-case basis. Please fill out this form to request an extension.

I can’t view the additional resource links

Additional resources support and expand upon the content presented in each module. Please note that some resources require a journal subscription and/or fee to be paid by the viewer. Access to these publications is not provided with this course. I would encourage you to see if your company or organization has access to these databases.

I have completed the course.

How do I access my course certificate and badge?

Your certificate will be available within the course platform when you reach 100% completion for your course. Be sure to complete any unfinished lessons and be aware that assignments need to be approved by a Schrödinger scientist before an assignment lesson is considered complete. When you complete the course, a badge will automatically be sent to the email address associated with your course registration with the subject line “Congratulations, you earned a badge!”.

What are the computer requirements and the cost of the Maestro program for individual use?

Jobs through this introductory course use a 4CPU node with 7200 memory. If you would like additional details for running locally on your own machine, please email You may also find this Documentation Page useful that dives into hardware requirements for running Schrödinger’s Maestro. Please request sales information here.

Will the material still be available after the course ends?

While access to the software will end when the course closes, some of the material within the course (slides, papers, tutorials, and scripts) are available for download so that you can refer back to it after the course. Other materials, such as videos and quizzes on the course platform, will be available for 2-3 months following the end of your course session.