Knowledge Base

Results

1521 results

My license server fails to start, and has the following log message: "Not...

August 11, 2016
The full text for this issue that you will see in the lmgrd.log file is:14:36:06 (lmgrd) "MachineName_Real": Not a valid server hostname, exiting.14:36:06 (lmgrd) Valid license...

Why do I get an error when trying to install Schrodinger software on a Windows...

October 25, 2013
This is a known issue with Windows and network drives. For workarounds, see http://support.microsoft.com/kb/927063

How do I restart or extend Desmond jobs from the command line?

September 16, 2021
You can restart a single Desmond simulation to continue from where it stopped or to extend the length of the simulation by using the checkpoint (.cpt) file. Desmond jobs can...

How do I set an environment variable?

September 30, 2019
You can set an environment variable on a Linux, Windows, or Mac platform with the instructions given below. If you want to use Schrödinger applications using the command line,...

How do I configure my schrodinger.hosts file for Desmond GPU jobs?

September 24, 2021
First ensure that you have configured your machine and software, as described in article 1834. Single Host Configuration To make use of GPU cards for Desmond calculations,...

I cannot save edits to schrodinger.hosts on my Windows machine. Why is this?

November 13, 2013
Files installed into "Program Files" or "Program Files (x86)" typically require administrative privileges to edit. This is the location where Schrödinger software is...

How do I design a covalent docking custom reaction type?

October 13, 2017
To design and use a custom reaction type in your covalent docking run, you can use a set of keywords that specify the receptor reaction site, the ligand reaction site, and the...

How can I run a well-tempered metadynamics simulation with Desmond?

May 27, 2021
Setup of well-tempered metadynamics simulationsWell-tempered metadynamics simulations can be setup and run with the following steps:Set up the metadynamics job as usual in Maestro...

How can I moderate the use of my licenses, so that my jobs don't run out...

July 15, 2019
Some of the supported batch queues have a license checking mechanism that can be enabled. This mechanism allows the queue to manage the licenses as a resource, and protects jobs...

How can I reduce the size of my Desmond trajectory?

November 14, 2019
Use the trj_merge.py script and the -s START:END:STEP option. For example: $SCHRODINGER/run trj_merge.py -s 0:100:10 md-out.cms md_trj -o sliced This will write every tenth...

I am performing NMR calculations with Jaguar. What are the units of the...

February 12, 2014
The Shielding Tensor is given in ppm, parts per million.

My Jaguar jobs die with an MKL FATAL ERROR message for loading the function...

February 12, 2014
Errors of this sort are usually due to library conflicts. You may have settings in your PATH or LD_LIBRARY_PATH environment variables that are causing the conflicts. Unsetting...

I would like to find examples of the usage of a certain KNIME node, or find an...

June 23, 2014
Use the Workflow list node in the Schrödinger extensions. In addition to the node, there is a very useful example workflow called "Workflows in the current workspace",...

How can I obtain a Z-matrix representation of my Cartesian input coordinates? I...

February 16, 2015
In the Jaguar panel, click the arrow next to the Settings button (gear icon) at the bottom right of the panel, and choose Edit. In the Edit Job dialog box, select the Structure...

I want to run vibrational frequency calculations in QSite, but this option is...

March 3, 2014
QSite vibrational frequency calculations are not available for frozen orbital (Entire Residue or Side Chain) cuts. If you want to perform frequency calculations, use the Free...

When performing a Jaguar geometry optimization with the PBF method (isolv=2...

March 3, 2014
In principle, a geometry optimization should arrive at an energy minimum. In practice, this result is sometimes hard to achieve due to the complex or shallow potential energy...

My Jaguar jobs are failing with an error "No space left on device"....

June 15, 2016
If the disk where you are writing the files has a lot of other files, you should consider cleaning up the other files to make space. Otherwise, the best way to deal with this...

Do you have any Jaguar benchmarks, with respect to performance?

September 2, 2019
Computational performance depends on a lot of factors, so it is useful to perform your own tests on your machine to obtain accurate performance and scaling information.However we...

How many ligands do I need to develop a QSAR model using Phase?

March 31, 2014
We would consider about 30 ligands to be a minimum to create a QSAR model, with 75% in the training set and 25% in the test set.

When I try to import readline in the Python interactive window on my Mac, it...

April 1, 2014
The Schrödinger suite includes a full Python distribution, but unfortunately the readline package is not compatible with OS X 10.9 Mavericks. To work around this problem,...


Not finding what you need? Request a new KB article.

Back To Top