The routine essentially produces Ramachandran plots but has no 2D contour graphical output. As well as a multi-file output which can be examined in the main graphics (ASTRAL), it produces table output which can be processed by other graphical packages. Its main use has been to simulate (and hopefully understand) rotational barriers in conjunction with nmr data. Other applications have included examining the changes of rotational barriers when under the influence of regular changes of substitution pattern e.g. looking at peptide phenyl rotations when the aromatic is o-F, m-F & p-F substituted.
Clicking the Spin Barrier button generates a new window.
The information and questions are hopefully self-explanatory. Just follow them, answering appropriately. The input is via keyboard. To get the atom numbers, shift and resize the new window so that you can see the molecule in the main screen, activate 'label' and enter the information in the new window.
One multi-file is produced, named according to the spin request. Thus :
The log file, with the listing of the output energies (in kcal/mole) is in the mail.
Remember to work out a sensible rotation increment. If, for example, you ask for 3 bond spins at 10 degree increments over 360 degrees each, on a small molecule of 25 atoms, stored as a 2300 byte file, you will land up with a .ss3 file of 363.2300 bytes = 107 Megs!! This size of file cannot be coped with.......
This procedure is used in the conformational hunter but is made available on its own for convenience. Usually. molecular dynamics places kinetic energy into each bond to give velocity and acceleration to each atom- crudely simulating ir normal modes. The time step is 1fs (10-15 second). This routine places the energy in the torsional twist of each bond and, although rendering meaningless the time interval and 'reality' of the system, gives rise to movements more likely to be seen on the nmr time scale and hence of much more use to the practical chemist. The procedure is quite fast and is often run on-line (see BATCH)
Generate a new window by clicking on the button.
Specify an output filename (it will be designated a .dst file)
The temperature may be very high if you want to see rare conformers. Up to 10000K has not caused problems.
The number of cycles and the collection interval are up to you- but remember that the final file should be restricted to 500 structures or so, if it is to be handled without difficulty.
The log file, with the listing of the output energies (in kcal/mole) is in the mail.
