SGE Cluster Docking
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SGE Cluster
- Head Node
'sgehead.compbio.ucsf.edu' is the submit machines name.
- SGE Commands
qsub: submit jobs
qstat: check job status
qdel: remove jobs
qhost: check cluster status
man sge_intro: start of manpage documentation
- Docking Workflow
| ssh sgehead.compbio.ucsf.edu | #ssh to SGE submit machine |
| mkdir example | #make docking directory |
| cd example | #change to docking directory |
| cp <somedir>/rec.pdb . | #copy or create rec.pdb |
| cp <somedir>/xtal-lig.mol2 . | #copy or create xtal-lig.mol2 (or even xtal-lig.pdb) |
| touch .only_spheres | #stop after grid generation |
| startdockblaster4 | #create spheres and grids |
| cp calibrate/INDOCK.1.A INDOCK | #copy or create INDOCK |
| mksdir2.csh 2 50 | #create directories for fragment-like in ~50 chunks |
| cd run.2 | #chdir into run directory |
| startdockbks3 | #submit database chunks to SGE cluster |