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.

• Naccess Main Site: http://www.bioinf.manchester.ac.uk/naccess/

• Module Name: naccess (see the modules page for more information)
• Singlethreaded
• Reference data in /pdb/pdb/

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 ~]$

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

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 naccess