Molecular software: Difference between revisions
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It should be stressed that due to paid licences to Floris's name, people outside the SOC who still would like to use the machine will have to add Floris to their list of authors upon publication. | It should be stressed that due to paid licences to Floris's name, people outside the SOC who still would like to use the machine will have to add Floris to their list of authors upon publication. | ||
== Applying for access to the | == Applying for access to the Molecular Chemistry cluster == | ||
The SOC cluster shares its computing power with the spectroscopy and catalysis group from Jana Roithova. In order to get access you first need a science account with which you can access the lilo login server (more details on: https://cncz.science.ru.nl/nl/howto/ssh/). Afterwards you need to be added to the group '''molmech''' before you can access cn142 (the main SOC cluster node), which is currently governed by wtitulaer. More information on using the cluster node can be found at [ | The SOC cluster shares its computing power with the spectroscopy and catalysis group from Jana Roithova. In order to get access you first need a science account with which you can access the lilo login server (more details on: https://cncz.science.ru.nl/nl/howto/ssh/). Afterwards you need to be added to the group '''molmech''' before you can access cn142 (the main SOC cluster node), which is currently governed by wtitulaer. More information on using the cluster node can be found at [[Molecular chemistry cluster]]. | ||
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|CHARMM || Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory, performing protein-ligand modelling tasks || Academic, personal || cn103, cn142 | |CHARMM || Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory, performing protein-ligand modelling tasks || Academic, personal || cn103, cn142 | ||
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|[[Chimera]] || Molecular modelling visualization program || Academic || cn142 | |||
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|DOCK 3.8 || Molecular docking of large-scale libraries (known as virtual screening). || Academic, personal || cn142 | |DOCK 3.8 || Molecular docking of large-scale libraries (known as virtual screening). || Academic, personal || cn142 | ||
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|Gromacs || Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory and analyzing trajectories. | |Gromacs || Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory and analyzing trajectories. | ||
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|MOE || Variety of medicinal chemistry related operations such as: QSAR, Pharmacophores, Homology Modelling, (template-based) Docking, Protein modelling, Fragment-growing, Library enumeration. Interfaces to Gaussian, AMBER, NAMD are available. || Rutjes group || cn142 | |MOE || Variety of medicinal chemistry related operations such as: QSAR, Pharmacophores, Homology Modelling, (template-based) Docking, Protein-ligand modelling, Fragment-growing, Library enumeration, Visualization program. Interfaces to Gaussian, AMBER, NAMD are available. || Rutjes group || cn142 | ||
|- | |- | ||
|NAMD || Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory. | |NAMD || Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory. | ||
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|YASARA Structure || Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program || Academic wtitulaer personal || cn142 | |||
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Latest revision as of 15:22, 28 June 2024
The SOC has access to a variety of chemistry related softwares. Some of these come with paid licenses however as well as some requiring hardware the general user laptop doesn't have. Therefore, the SOC has a dedicated computing cluster running under maintenance by C&Cz and has a computer workstation where visual programmes can more easily be ran from. This page serves as a guide how to get access to these systems as well as providing an overview of the lab's current running softwares.
Applying for access to the SOC workstation
Application for the SOC-workstation requires sending an email to socmoe-access@science.ru.nl, after which you will receive a document[make link] to read prior to accessing the workstation. It should be stressed that due to paid licences to Floris's name, people outside the SOC who still would like to use the machine will have to add Floris to their list of authors upon publication.
Applying for access to the Molecular Chemistry cluster
The SOC cluster shares its computing power with the spectroscopy and catalysis group from Jana Roithova. In order to get access you first need a science account with which you can access the lilo login server (more details on: https://cncz.science.ru.nl/nl/howto/ssh/). Afterwards you need to be added to the group molmech before you can access cn142 (the main SOC cluster node), which is currently governed by wtitulaer. More information on using the cluster node can be found at Molecular chemistry cluster.
(Currently) available softwares
This table should list all softwares available. Should your desired software not be on the list, please contact wtitulaer to see what is possible.
| Software | Usual purpose(s) | License-type | Nodes installed |
|---|---|---|---|
| AMBER24 | Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory, analyzing trajectories and performing other protein-ligand modelling tasks | Academic, personal | cn142 |
| CHARMM | Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory, performing protein-ligand modelling tasks | Academic, personal | cn103, cn142 |
| Chimera | Molecular modelling visualization program | Academic | cn142 |
| DOCK 3.8 | Molecular docking of large-scale libraries (known as virtual screening). | Academic, personal | cn142 |
| Gaussian | Small molecule calculations on DFT level of theory such as geometry optimizations and predicting IR-spectra from these. | ||
| GOLD | More precise molecular docking via genetic algorithm (GA) pose sampling | Academic, RU-broad from solid state chemistry | cn142(?) |
| Gromacs | Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory and analyzing trajectories. | ||
| MOE | Variety of medicinal chemistry related operations such as: QSAR, Pharmacophores, Homology Modelling, (template-based) Docking, Protein-ligand modelling, Fragment-growing, Library enumeration, Visualization program. Interfaces to Gaussian, AMBER, NAMD are available. | Rutjes group | cn142 |
| NAMD | Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory. | ||
| YASARA Structure | Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program | Academic wtitulaer personal | cn142 |