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Keck II Center: Software

See FAQ for information about getting specific software installed.
Besides the usual end-user software, several applications are installed on the Keck II workstations. If you are interested in using software that is not on this list, please contact keck-help @ keck2.ucsd.edu.

Software list by package name
Package Platforms Commands Paths Environment Setup and Notes
AMBER v8 Linux See exe directory under path /soft/linux/pkg/amber N/A
APBS v0.4.0 Linux See bin directory under path /soft/linux/pkg/apbs/bin/ N/A
Arp/Warp v6.0 Linux See bin directory under path /soft/linux/pkg/arp_warp setup_arpwarp1)
SGI /soft/sgi/pkg/arp_warp
AutoDock v3.0.5 Linux autodock3, autogrid3, addsol /soft/linux/pkg/AutoDock limit stacksize unlimited2)
SGI /soft/sgi/pkg/AutoDock N/A
Sun /soft/sun/pkg/AutoDock N/A
AutoDock Tools (MGLTools) v1.4.1 Linux adt, pmv, vision /soft/linux/pkg/MGLTools setup_mglt1)
SGI /soft/sgi/pkg/MGLTools
Catalyst v4.60 SGI catalyst /soft/sgi/pkg/msi Available databases: NCI200, Maybridge99. Note 3 and 5.
CCP4 v5.0.1 Linux See bin directory under path /soft/linux/pkg/ccp4 setup_ccp41)
SGI /soft/sgi/pkg/ccp4
CHARMM v32 Linux See bin directory under path /soft/linux/pkg/c32b1 N/A
Crystallography and NMR System (CNS) v1.1 Linux cns /soft/linux/pkg/cns_solve setup_cns1)
SGI /soft/sgi/pkg/cns_solve
SUN /soft/sun/pkg/cns_solve
cns2fsfour v1.02 Linux cns2fsfour /soft/linux/bin N/A
SGI /soft/sgi/bin
SUN /soft/sun/bin
Cambridge Structural Database Linux cq, mercury, mogul /soft/linux/pkg/cambridge setup_csd1)
DL_POLY v2.13 Linux dlpoly /soft/linux/pkg/dl_poly Please see the license before using.
SGI /soft/sgi/pkg/dl_poly
SUN /soft/sun/pkg/dl_poly
DLPROTEIN v2.1r1 Linux dlprotein /soft/linux/pkg/dlprotein Please see the license before using.
SGI /soft/sgi/pkg/dlprotein
SUN /soft/sun/pkg/dlprotein
Data Explorer (OpenDX) v4.1.3 SGI dx /soft/sgi/pkg/dx setup_opendx1)
SUN /soft/sun/pkg/dx
EPMR v2.5 Linux epmr_* /soft/linux/pkg/epmr N/A
SGI /soft/sgi/pkg/epmr
FELIX SGI felix /soft/sgi/pkg/msi Note 3, 5 and 6.
Linux /soft/linux/pkg/msi
Gamess March-24 2007.R3 Linux gamess.01.x /soft/linux/pkg/gamess N/A
Gamma SUN gamma4A N/A N/A
Gaussian 03 vB.04 Linux g03 /soft/linux/pkg/g03 setup_g031)
Gaussian 98 vA7 Linux g98 /soft/linux/pkg/g98 setup_g981)
SGI /soft/sgi/pkg/g98
SUN /soft/sun/pkg/g98
GaussView v3.09 SGI gview /soft/sgi/pkg/gv setup_gv1)
GeomView v1.8.2-rc8 Linux geomview /soft/linux/pkg/geomview/bin N/A
Grace v5.1.4. Linux xmgrace /soft/linux/pkg/grace N/A
SGI /soft/sgi/pkg/grace
Grasp v1.3.6 SGI grasp /soft/sgi/pkg/grasp N/A
Illustrator v9.0 Windows N/A N/A N/A
Matlab v6.5.1 (R13SP1) Linux matlab /soft/linux/bin N/A
SGI /soft/sgi/bin
SUN /soft/sun/bin
ModelFree v4.10 SGI modelfree /soft/sgi/pkg/ModelFree N/A
Modeller v6.2 Linux mod6v2 /soft/linux/pkg/modeller setup_modeller1)
SGI /soft/sgi/pkg/modeller
SUN /soft/sun/pkg/modeller
Molden v4.0 Linux molden /soft/linux/bin N/A
SGI /soft/sgi/bin
SUN /soft/sun/bin
MolMol SGI molmol /soft/sgi/pkg/molmol N/A
Sun /soft/sun/pkg/molmol
MolScript v2.1.2 SGI molscript.exe /soft/sgi/pkg/molscript N/A
NAMD v2.3b2 Linux charmrun namd2 /soft/linux/pkg/NAMD N/A
NMRpipe SGI nmrPipe, nmrDraw /soft/sgi/pkg/NMRpipe setup_nmrpipe1)
Sun /soft/sun/pkg/NMRpipe
NMRView v5.0 Linux nmrview /soft/linux/bin/ setup_nmrview1)
SGI /soft/sgi/bin/
SUN /soft/sun/bin/
NWChem Linux See bin/LINUX directory /soft/linux/pkg/nwchem N/A
Office 2000 Windows N/A N/A N/A
O v7.0.1/v8.0.5 Linux ono /soft/linux/pkg/o_v7.0/bin, data Please read the license agreement.
The 8.0.5 version is in o_v8.0 directory
SGI /soft/sgi/pkg/o_v7.0/bin, data
SUN /soft/sun/sgi/o_v7.0/bin, data
Phaser v1.2 Linux phaser /soft/linux/pkg/phaser/bin N/A
SGI /soft/sgi/pkg/phaser/bin
Pipe2Flx v1.03a SGI pipe2flx /soft/sgi/pkg/pipe2flx/bin/ N/A
Photoshop 6.0 Windows N/A N/A N/A
Pymol v0.98 SGI pymol.com /soft/sgi/pkg/pymol N/A
Raster3D SGI render /soft/sgi/bin, /soft/sgi/pkg/Raster3D/ N/A
Ribbons v3.15 Linux ribbons /soft/linux/pkg/ribbons setup_ribbons1)
SGI /soft/sgi/pkg/ribbons
SUN /soft/sun/sgi/ribbons
SigmaPlot 2001 Windows N/A N/A N/A
Sax suite SGI crysol23s, dammin43s, gasbor12s, gnom44s /soft/sgi/pkg/Sax N/A
SnB SGI SnB /soft/sgi/pkg/snb setup_snb1)
ShelX Linux shelx* /soft/linux/bin/ N/A
SGI /soft/sgi/bin, /soft/sgi/pkg/ShelX
SIMMOL v1.0.0 Linux simmol /soft/linux/pkg/simmol/bin/ N/A
SIMPSON v1.1.1 Linux simpson /soft/linux/pkg/simpson/ N/A
sparky v3.106 Linux sparky /soft/linux/pkg/sparky/bin N/A
SGI /soft/sgi/pkg/sparky/bin
SUN /soft/sun/pkg/sparky/bin
spscan v1.0.62a SGI spscan /soft/sgi/pkg/spscan setup_spscan1)
ultrascan v5.0 Linux us /soft/linux/pkg/us-5.0 setup_ultrascan1)
USF software Linux N/A /soft/linux/pkg/USF N/A
SGI /soft/sgi/pkg/USF
Visual Studio Windows N/A N/A N/A
VMD v1.7 Linux vmd N/A N/A
SGI
SUN
XEasy v1.3.13 SGI xeasy /soft/sgi/pkg/XEasy setup_xeasy1)
XPLOR-NIH v2.9.2 Linux xplor /soft/linux/pkg/xplor-nih N/A
SGI /soft/sgi/pkg/xplor-nih
XtalView v4.1 SGI xtalmgr /soft/sgi/pkg/XtalView setup_xtalview1) Note 4.

Notes:
1. Type this command to set up proper environment before using the application.
2. Put this line into your .tcshrc or execute before running the code.
3. Only limited number of licenses is available.
4. For using stereo visualization hardware with this application see Stereo how-to.
5. All Accelrys documentation is locally accessible at /soft/sgi/pkg/msi/msi_docs. Use your web browser to read it.
6. To run felix on serrra:
# source /soft/linux/pkg/msi/cshrc
# set_context Felix2004
# felix

Please direct any questions or comments to keck-help @ keck2.ucsd.edu
Last modified: October 10 2007 12:22:11 pm.