Restraint checking

The AQUA program first tries to find all restraint atoms in the atom set read from the coordinate file. It also checks the validity of the bound values. This may result in error messages. Examples are:

External atom name not found: .....

* Can't match residue for this atom: .....

and the corresponding final output message:

* One or more restraint atoms could not be found in the structure

In the second phase, the program performs extensive checking of the restraint list. You may see messages such as:

Combining bounds of:

restraint # .....

indicating that a pair of restraints has been found, of which one sets the upper bound and the other sets the lower bound. AQUA counts such a pair as one restraint. The restraint numbers refer to a sequential numbering of restraints in the order in which they appear in the restraint file. The final output message will say something like:

* .. Restraints collapsed into .. because upper and lower bounds were

* specified separately

Restraint checking may also produce warning/error messages:

* Repeated restraint:

* restraint # .....

* Bound values differ in identical restraints (keeping the tightest bounds):

* restraint # .....

Warning: bound skipped because atom(s) could not be found

restraint # .....

* Error: upper bound < lower bound

* restraint # .....

These messages explain themselves. In the first two cases, the duplicated restraint is dropped. In the last two cases the offending restraint is skipped.

The final output summarizes the numbers of skipped and merged restraints.

You can switch off the search for duplicated restraints by using the set multiple off option, see 'qhelp options'.