Step 2. How to run qconvert

The qconvert script converts a restraints file to AQUA format, and simultaneously splits the file into NOE, hydrogen bond, disulphide, generic distance and torsion angle components.

Before running qconvert, you will need to initialize the AQUA environment variables (see AQUA Initialization). This is most easily done by simply typing:

aqua

To run qconvert, enter:

qconvert [-r restraint_prefix] [-t file_type] restraint_file

where:

restraint_file is the name of the restraints file to be converted into AQUA format, and should include the full path unless the file is in the default directory. (If the restraints are in several files, see below).
[-r restraint_prefix] optionally sets the value of restraint_prefix which is the root name of all the files output by qconvert, namely:
If the -r option is not used, the restraint_prefix is taken from the restraint_file name by stripping away the extension and path.
[-t file_type] is a number (currently 1, 2, 3, 4 or 99) which optionally tells qconvert the file format of the input restraint file, namely:
If the -t option is not used, the file_type is determined automatically from the contents of the file (if possible).

Information of additional options can be obtained by typing qconvert on its own (ie without any parameters), or by reading the qconvert manual page.

Note: the order in which optional arguments are given is unimportant.

When the restraints are in several files

If the restraints reside in different files, the user should take care to give all converted files the same restraint_prefix if the AQUA analysis is to take into account all data.

For example, if we have two restraint files called mynoes.tbl and mytor.tbl, conversion can be accomplished by:

qconvert mynoes.tbl

qconvert -r mynoes mytor.tbl

giving converted files mynoes.noe and mynoes.tor. Since this particular restraint_prefix is rather confusing, a better alternative is something like:

qconvert -r mydata mynoes.tbl

qconvert -r mydata mytor.tbl

giving converted files mydata.noe and mydata.tor.

Note: the extension .tbl does not have any special meaning for AQUA. Any extension, or no extension at all, may be used for the original restraint file.