Difference between revisions of "Dock"
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|{{#vardefine:url|http://dock.compbio.ucsf.edu}} | |{{#vardefine:url|http://dock.compbio.ucsf.edu}} | ||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
| − | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | + | |{{#vardefine:conf|1}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> |
| − | |{{#vardefine:pbs| | + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> |
|{{#vardefine:policy|}} <!--Enable policy section --> | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
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*dock | *dock | ||
| − | === | + | ===Parallel (MPI)=== |
*intel | *intel | ||
*openmpi | *openmpi | ||
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_DOCK_BIN - executable directory | * HPC_DOCK_BIN - executable directory | ||
* HPC_DOCK_DOC - documentation directory | * HPC_DOCK_DOC - documentation directory | ||
| + | * HPC_DOCK_PARAMETERS - directory for parameters | ||
| + | |||
<!--Additional--> | <!--Additional--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
| + | <!-- | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | --> | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
Latest revision as of 20:48, 2 August 2021
Description
DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.
Required Modules
Serial
- intel
- dock
Parallel (MPI)
- intel
- openmpi
- dock
System Variables
- HPC_DOCK_DIR - installation directory
- HPC_DOCK_BIN - executable directory
- HPC_DOCK_DOC - documentation directory
- HPC_DOCK_PARAMETERS - directory for parameters