Naccess on Biowulf
Briefly, the naccess program calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface. This program is an implimentation of the method of Lee and Richards (1971) J.Mol.Biol.55, 379-400. which does just that. The program is dimensioned for up to 20000 atoms, and allows the variation of the probe size and atomic radii by the user.
Documentation
- Naccess Main Site: http://www.bioinf.manchester.ac.uk/naccess/
Important Notes
- Module Name: naccess (see the modules page for more information)
- Singlethreaded
- Reference data in /pdb/pdb/
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ ml naccess [+] Loading naccess 2.1.1 ... [user@cn3144 ~]$ zcat /pdb/pdb/cr/pdb1crn.ent.gz > 1crn.pdb [user@cn3144 ~]$ naccess 1crn.pdb naccess: using defualt vdw.radii naccess: using default STD FILE [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. naccess.sh). For example:
#!/bin/bash module load naccess naccess /path/to/blah.pdb
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] naccess.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. naccess.swarm). For example:
naccess 1pdb.pdb naccess 2pdb.pdb naccess 3pdb.pdb naccess 4pdb.pdb
Submit this job using the swarm command.
swarm -f naccess.swarm [-g #] [-t #] --module naccesswhere
-g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
-t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
--module naccess | Loads the naccess module for each subjob in the swarm |