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Page updated on
Oct 19 2010
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on a Mac and powered by Linux

Laboratory for Molecular Simulation
Director: Michael B. Hall Manager: Lisa M. Pérez
Phone: (979) 845-9384Fax (979) 845-2971Rm. 2109 Chemistry
e-mail: mouse@chem.tamu.edu

Cerius2
by Accelrys, Inc.

Cerius2 is a user-friendly graphical molecular modelling program developed by Accelrys Inc. (formerly MSI) that incorporates a wide variety of popular molecular modelling codes in materials sciences, life sciences and drug design. The Laboratory for Molecular Simulation, in collaboration with faculty in the departments of Chemistry, Biochemistry & Biophysics, Chemical Engineering, and Environmental Engineering, has purchased licenses for a large number of the modules available in cerius2.

Cerius2 is now legacy software and is no longer supported by Acclerys. Most of the Cerius2 license have been converted to Materials Studio, the program developed by Accelrys to replace Cerius2.

Cerius2 Homepage Running Cerius2 Licenses Patches Trouble-Shooting

Running Cerius2

The current version of Cerius2 for SGI/IRIX machines is 4.10

To run cerius on your sgi machine you will need to add the following line to your .tcshrc file

alias   cerius   '/chem/cerius/cerius2/bin/cerius2'

To start the program from your SGI machine you will need to source your .tcshrc file to activate the new alias (source .tcshrc) and then type: cerius at the prompt.

If you would like to run an older version of Cerius2 for SGI/IRIX, you will need to add additional aliases to your .tcshrc file:

alias  cerius2vversion  '/chem/cerius/cerius2_version/bin/cerius2'

where version should be replaced with one of the available versions: 3.8, 4.8 or 4.9

For example, if you would like to run Cerius2 4.9, you should create the following alias:

alias  cerius2v4.9  '/chem/cerius/cerius2_4.9/bin/cerius2'

The current version of Cerius2 for Linux is 4.11

To run cerius on your linux machine you will need to add the following line to your .tcshrc file

alias   cerius   '/chem/cerius/cerius2L/bin/cerius2'

note: The linux version of Cerius2 does not contain all of the programs available in the IRIX version. Specifically, all of the quantum modules are missing except the mopac module


Modules Available For Use Through The LMS
Module name Number of Licenses
ADF (Amsterdam Density Functional)* 1
Amorphous Builder 0
Cation Locator 2
CASTEP 0
CFF Force Field 12
COMPASS 0
Confomers 0
Crystal Builder 3
Descriptor+ 0
Diffraction-Amorphous 1
Diffraction-Crystal 1
Diffraction-Faulted 2
Discover 0
DLS (Distance Least Squares) 1
DMol3 0
DSolid 0
DMol3 Interface 0
Dynamics 1
ESOCS 0
Fast Structure 0
Force Field Editor (FFE) 2
Genetic Algorithms 0
Guassian Interface 1
HRTEM 1
Interface Builder 2
IR/RAMAN 1
LEED/RHEED 1
Mechanical Properties 1
Minimizer 1
MOPAC 16
Open Force Field 5
Powder Indexing 1
Polymer Builder 1
Polymer Properties 1
QSAR+ 0
Rietveld (DBWS/GSAS) 0
SDK (Software Developer kit) 1
Sorption 1
Structure Predictor 2
Surface Builder 1
Visualizer 1
Zindo 0
*Only works in Cerius2 3.8

Trouble-shooting:

If you receive the error: cerius - command not found

type: source .tcshrc at the prompt and try again. If you still receive a command not found error, you need to check the alias in your .tcshrc file to make sure that it is properly defined. If your alias is correct then you should check to see if the /chem directory has been mounted on your machine by typing df at the prompt.

If /chem is not listed in the column under 'Mounted on', it is not mounted on your machine you will need to mount it before you can run the cerius program.

If /chem has been mounted on your machine in the past you will need to login as root and type: /sbin/mount -h chmsgi

if this does not mount /chem (type df to determine if /chem is mounted) check to make sure that you have the following line in your /etc/fstab file: chmsgi.chem.tamu.edu:/chem  /chem  nfs  soft,intr,bg 0 0

If this line is in your fstab file and you still cannot mount /chem on your machine, contact your system administrator.

If you are running on a remote machine and you receive the error:

Xlib: connection to "labmol4.chem.tamu.edu:0.0" refused by server
Xlib: Client is not authorized to connect to Server
Error: Can't open display:labmol4.chem.tamu.edu:0.0

(where labmol4 will be replaced by the local machine name)

You need to make sure that you use the -X flag when you ssh to the remote machine ( ssh -X username@remote_machine_name )
If you are accessing the remote machine from a Linux box, you will probably need to use both the -X and -Y flags when you ssh to the remote machine.