Step 3. How to run AQUA

Before running AQUA, you will need to initialize the environment variables - if you have not already done so (see AQUA Initialization). This is most easily done by simply typing:

aqua

Then, to run AQUA, enter:

aqpc [-c] [-r restraint_prefix] coordinate_file [ranges-file]

where:

coordinate_file is the name of the coordinates file in either PDB or BIOSYM format (car or multi-line arc).
The name of the coordinate_file provides a project name for aqpc. This project name is derived from coordinate_file by removing extension and path.
The root name of all output files is the project name. The file name extension of the output files indicates the type of data the file contains:
```
    summary:     .nsm (noe), .hsm (hb), .ssm (ss), .dsm (dis)
    violations:  .nrv (noe), .hrv (hb), .srv (ss), .drv (dis)
    counts:      .nrc (noe), .hrc (hb), .src (ss), .drc (dis)
```
[ranges-file] is the name of an (optional) file specifying which models and residue ranges are to be included in the calculations (see Selecting model- and residue-ranges).
[-r] is used to specify the restraint prefix of the converted restraint file(s). It can be omitted if restraint prefix and project name are identical.
[-c] prevents cleanup of the working files. This will speedup the calculation if you repeat the analysis for coordinate_file, e.g. with a different restraint file or a (different) ranges-file. (Note that in this case the output files will be overwritten since they have the same project name!). If, however, the contents of coordinate_file have changed all intermediate files should be removed before repeating aqpc; this may be accomplished by the qclean command. See Using qclean for some more details.

Example

If the AQUA restraint files were produced by (see Run qconvert):

qconvert -r mydata mynoes.tbl

qconvert -r mydata mytor.tbl

then the analysis command would be:

aqpc -r mydata myprot.pdb

giving output files myprot.nsm, myprot.nrv etc.

Further information

For details of AQUA outputs and errors messages, see AQUA outputs and analysis tools.

The output data of the analysis can be visualized with PROCHECK-NMR (see How to run PROCHECK-NMR).

Currently, AQUA does not calculate violations of torsion angle restraints, but these can still be visualized with PROCHECK-NMR. (Given the way PROCHECK-NMR works aqpc has to copy the restraint file to reflect the difference between restraint prefix and project name, i.e. in the example mydata.tor is copied to myprot.tor).