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:
Then, to run AQUA, enter:
aqpc [-c] [-r restraint_prefix] coordinate_file [ranges-file]
coordinate_file is the name of the coordinates
file in either PDB or BIOSYM format (car or
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
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.
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.
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).