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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:



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

then the analysis command would be:

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).

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