This docker brings one movable (but conformationally fixed) molecule together with a fixed (and conformationally fixed) molecule from every direction using a free SIMPLEX minimiser. The resulting multi-file contains all the local minimum energy docks which are thermodynamically possible. In 'real life', kinetic energy would ensure that each local dock minimum would have many chances to relaunch its molecule until only a final best global dock results.
As a general rule, the best dock- (that with the lowest energy) - is the global best dock position. The advantage of retaining all local docks is that the patterns and paths of docking can be viewed and some statistical data gleaned from counting how many common docking positions result from many different paths.
For best results, add XEDs to the input molecules after charging them with ACCs from the Minimise/Charge button.
You will first be asked to specify a mobile molecule (usually the smaller of the two), followed by the fixed molecule. Neither corresponds to the structure on screen. Both need to be built, prepared and filed with a name before starting the Dock procedure (see Book 7).
Usually, the mobile molecule is allowed to approach the fixed from some distance away ('outside'). We have had occasion to test what happens to occluded systems - a solvent caught inside a cage zeolite or 'Rebek Tennis Ball'. When this is required, the patterns obtained from starting the docking from outside the fixed molecule can be very different from starting the docking from inside the fixed (cage).
The question about start position depends very much on your system.
Set the dielectric. A chance to vary this is often very important in docking experiments.
Send the job to BATCH by defaulting and keep an eye on the CPU ('tops' or 'osview') and your mail. A log of the process will appear in the mail when all is finished.
Nore: As already described, the input to this procedure is two molecules - a mobile or bullet and a fixed or target. It produces one multi-file and a log file. The multi-file can be viewed in the main screen (ASTRAL). The log file is a text file. (Remember that there is always some logging output in your mail) :
.kst contains all locally minimised docks of bullet on target (about 260 molecules)
.ks1 contains the log of the run and a statistical analysis of the experiment.
The input procedure is much the same as 'Dock 2 Molecules'. In order to gain some idea of the build-up of a mobile molecule onto a fixed one, the simple dock process has been modified such that the best docked mobile and its target from the 2 molecule dock process are extracted after the 1st run and the binary complex used as the next target. This can be done many times, each time with the target growing as one more mobile is added to it. The process has been designed to investigate solvent shells but can sequentially dock any two molecules.
For best results, add XEDs to the input molecules after charging them with ACCs from the Minimise/Charge button.
You will first be asked to specify a mobile molecule (usually the smaller of the two), followed by the fixed molecule. Neither corresponds to the structure on screen. Both need to be built, prepared and filed with a name before starting the Dock procedure (see Book 7).
The sequential docking takes many hours. For 40 waters to solvate a small t-butyl ammonium cation, the batch job ran for about 24 hours on a 4000 (100MHz) SGI!
Set the dielectric. A chance to vary this is often very important in docking experiments.
Usually, the mobile molecule is allowed to approach the fixed from some distance away ('outside'). We have had occasion to test what happens to occluded systems - a solvent caught inside a cage zeolite or 'Rebek Tennis Ball'. When this is required, the patterns obtained from starting the docking from outside the fixed molecule can be very different from starting the docking from inside the fixed (cage).
The question about start position therefore depends very much on your system.
Send the job to BATCH by defaulting and keep an eye on the CPU (tops or osview) and your mail. A log of the process will appear in the mail when all is finished.
Note: The procedure produces one multi-file and a log file. The multi-file can be viewed in the main screen (ASTRAL). The log file is a text file. (Remember that there is always some logging output in your mail) :
.seq contains all locally minimised docks of bullet on target (as many molecules as you asked to be docked + the target)
