Manual Specification of Non-Rotatable Bonds
The user can specify additional bonds to be non-rotatable, to supplement the ring bonds automatically identified by DOCK. Such a technique would be used to preserve the conformation of part of the molecule and isolate it from the conformation search. Non-rotatable bonds are identified in the Tripos MOL2 format file containing the molecule. The bonds are designated as members of a STATIC BOND SET named RIGID (see Tripos MOL2 Format).
Creation of the RIGID set can be done within Chimera. With the molecule of interest loaded into Chimera, select the portion of the ligand you would like to remain rigid. Then select on File > Save MOL2. Make sure the "Write current selection to @ SETS section of file" is checked and save the file.
Alternatively, the RIGID set can be entered into the MOL2 file by hand. To do this, go to the end of the MOL2 file. If no sets currently exist, then add a SET identifier on a new line. It should contain the text "@<TRIPOS>SET". On a new line add the text "RIGID STATIC BONDS <user> **** Comment". On the next line enter the number of bonds that will be included in the set, followed by the numerical identifier of each bond in the set.