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| wiki:software [2020/05/12 12:10] – [Amber] admin | wiki:software [2021/07/29 15:48] (current) – [Available Software] admin |
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| ====== Available Software ====== | ====== Available Software ====== |
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| The following scientific packages are installed on Keck Center workstations: | These are some of the scientific packages installed on Keck Center workstations: |
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| ^ Installed software ^ Version ^ Executable ^ | ^ Installed software ^ Version ^ Executable ^ |
| |[[http://ambermd.org|Amber]] | 20 |sander, pmemd, pmemd.cuda | | |[[http://ambermd.org|Amber]] | 20 |sander, pmemd, pmemd.cuda | |
| |[[http://avogadro.sourceforge.net/|Avogadro]] | 1.0.3 |avogadro | | |[[http://avogadro.sourceforge.net/|Avogadro]] | 1.0.3 |avogadro | |
| |[[http://www.poissonboltzmann.org/apbs|APBS]] | 1.5 |apbs | | |[[http://www.poissonboltzmann.org/apbs|APBS]] | 3.0.0 |apbs | |
| |[[http://browndye.ucsd.edu/|BrownDye]] | 2018.5.1 |bd_top | | |[[http://browndye.ucsd.edu/|BrownDye]] | 2.0 |bd_top | |
| |[[http://ivl.calit2.net/wiki/index.php/CalVR|CalVR]]| 2013.12.2 |CalVR | | |
| |[[http://www.ccdc.cam.ac.uk| Cambridge Structural Database]] | 2014 | cq | | |
| |[[http://www.charmm.org|charmm]] | c41b2 |charmm | | |[[http://www.charmm.org|charmm]] | c41b2 |charmm | |
| |[[http://daltonprogram.org/|Dalton]] | 2016.2 |dalton.x | | |[[http://daltonprogram.org/|Dalton]] | 2016.2 |dalton.x | |
| |[[http://www.gaussian.com/|Gaussview]] | 5.0.9 |gview.exe | | |[[http://www.gaussian.com/|Gaussview]] | 5.0.9 |gview.exe | |
| |[[http://www.gromacs.org/|Gromacs]] | 5.1.2 |gmx | | |[[http://www.gromacs.org/|Gromacs]] | 5.1.2 |gmx | |
| |[[http://kepler-project.org|Kepler]] | 2.4 |kepler.sh | | |
| |[[http://www.mathworks.com/products/matlab/|Matlab]] | 2018a |matlab | | |[[http://www.mathworks.com/products/matlab/|Matlab]] | 2018a |matlab | |
| |[[http://mgltools.scripps.edu/|mgltools]] | 1.5.7r1 |pmv | | |[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2020 |moe | |
| |[[http://www.clcbio.com/products/molegro/|MMV]]| 2.5.0 |mmv | | |
| |[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2019 |moe | | |
| |[[http://simtk.org/home/msmbuilder|MSMBuilder]]| 2.5 |misc. | | |[[http://simtk.org/home/msmbuilder|MSMBuilder]]| 2.5 |misc. | |
| |[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 2.13 |namd2 | | |[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 3.0 |namd3 | |
| |[[http://orcaforum.cec.mpg.de/|ORCA]] | 4.2.0 |orca | | |[[http://orcaforum.cec.mpg.de/|ORCA]] | 5.0.1 |orca | |
| |[[http://www.pymol.org|Pymol]] | 2.3.0 |pymol | | |[[http://www.pymol.org|Pymol]] | 2.4.0 |pymol | |
| |[[http://pyrx.sourceforge.net|PyRx]] | 0.9 |run.sh | | |[[https://www.rosettacommons.org/|Rosetta]] | 3.9 | | |
| |[[https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page|Relion]] | 2.0 |relion | | |[[http://www.schrodinger.com|Schrodinger]] | 2021 |maestro | |
| |[[https://www.rosettacommons.org/|Rosetta]] | 3.5 | | | |[[http://www.ks.uiuc.edu/Research/vmd|VMD]] | 1.9.4 |vmd | |
| |[[http://www.schrodinger.com|Schrodinger]] | 2019 |maestro | | |
| |[[http://vina.scripps.edu/|vina]] | 1.1.2 |vina | | |
| |[[http://www.ks.uiuc.edu/Research/vmd|VMD]] | 1.9.3 |vmd | | |
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| ====== How to use it ====== | ====== How to use it ====== |
