Maestro

Versatile molecular modelling environenment especially for drug design

Description

NOTE: Licensing for 2012 has changed. Edit or download the new license file from the Scientist's User Interface!

Maestro is a versatile molecular modelling environment especially for drug design. It can be used to build, edit, run and analyse molecules. Maestro is available for consortium members during 2012-2013. Please check below to see it you are allowed to use Maestro. Another, restricted feature but fully academic version of Maestro and Desmond is available also for non-consortium members: see below the Desmond chapter.

Maestro modules

The Maestro license consists of 30 floating license tokens and three separate license pools listed below.  Different modules use a different amount of license tokens (0-8). The following modules use specific licenses, i.e. it is possible to run 30 simultaneous Glide jobs, 10 Jaguar and 10 MacroModel jobs. The Maestro Interface and Desmond have additional licenses to make them effectively 'free'. More information of the Maestro modules can be found at the Schrödinger www page: www.schrodinger.com

It is possible for one user to take up all licenses. Please be considerate and monitor your resource usage. You can check the license usage, e.g. on Hippu with the following command:

maestro-lisenssit

Consortium

The usage is limited to the Consortium members. The current members are the groups of Ari Koskinen (Aalto Univ.), Antti Poso (UEF), Mark Johnson (ÅA), Petri Pihko (JYU), Olli Pentikäinen (JYU), and Henri Xhaard (UH). The licensing is IP-address based. To install Maestro locally, the researchers within the consortium should contact Atte and send the IP of the computer from which they want to use Maestro. The usage is restricted by the EULA.

Usage

It is recommended to download and install Maestro on your own computer (Linux or Windows). You can download it from Scientist's Interface (requires a user account at CSC).

You can also use Maestro remotely from hippu.csc.fi (or hippu3.csc.fi, hippu4.csc.fi). This is convenient with the CSC's new FreeNX/NoMachine service, which is superior to X-emulators used earlier for similar purposes. To use FreeNX, you need to install the NoMachine client, which is available free of charge. With that, log in to nxlogin.csc.fi, and from there to Hippu. In Hippu you initialise Maestro with

module load maestro

and then start it with

maestro

It is not recommended to run Maestro Vuori, but if you so choose, please don't run maestro in the login nodes, but start an interactive batch job: module load maestro; salloc -n 1 -t 4:00:00 srun maestro. The preferred way to work in Vuori is to run jobs directly in the batch queue, see below Standalone usage.

Standalone usage

The maestro modules can also be used from the command line. You can save the input files needed to run the job from Maestro, copy them to Vuori and then run them from the command line. Instructions are here.

Desmond

Although Desmond is available also in the suite provided by Schrödinger Inc. it is possible to use the Academic version obtained directly from D.E.Shaw research, which may have some additional features. That version can be used by all academics in Finland for academic research (please consult the license agreement). Instructions for using Desmond in Vuori or Murska can be found here. Have a look at the Desmond Tutorial (pdf) by Istvan Kolossvary.

Installation

Maestro can be run on a Linux or Windows computer. Download the appropriate files from the New Scientist's Interface and follow instructions there. You need to have an account at CSC to download the software.

Manuals, Tutorials, Online Presentations

The Maestro Installation has full manuals in html and pdf format.  The Schrödinger website also provides recorded presentations online, which you can watch on your computer.

Citation

Please cite the Maestro modules in all published work as described in the Module manuals. Jaguar, for example, should be acknowledged with:

Jaguar, version 7.6, Schrödinger, LLC, New York, NY, 2009.