On bonds, the fold number is simply the number of gross conformers. So for '3' there are assume 3 states, each 360/3=120 degrees apart. Thus each move is +- 120 degrees. A fold number of 2 would mean two conformers, each +- 360/2=180 degrees.
On atoms the fold number contains more specific information. An atom fold number of 3 means an "Osawa wag" is preformed. (A 4 implies a coupled osowa wag in a cyclohexane like ring.) In the case where the number contains 3 digits, the ones-digit is either 3 or 0 for Osawa wag or no wag, respectively. The hundred's digit, if present indicates that an inversion will be tried. This may occur on asymmetric, non-planar, trivalent nitrogens.
Use the keyword PRINTLEV=2 when the job is run to see more information on what precisely is being flipped and/or rotated.
Interpreting the output file:
Description of the columns:
c Cis c : -15 .. 0 .. 15 0.0 c+ c+ : 15 .. 30 .. 45 c- ~ -30 -30 | 30 g+ Gauche g+ : 45 .. 60 .. 75 g- ~ -60 -60 \|/ 60 p+ : 75 .. 90 .. 105 p- ~ -90 -90 -----*----- 90 p+ l+ : 105 .. 120 .. 135 l- ~ -120 -120 /|\ 120 t+ : 135 .. 150 .. 165 t- ~ -150 -150 | 150 l+ Trans t : 165 .. 180 ..-165 180 t+ t
|CONFANAL*||Do a conformational search producing multiple results.|
|SCONFANAL*||Do a conformational search producing only a single, lowest energy, result.|
|SLCONFANAL*||Menu command to generate a library of conformers. Similar to combining the following keywords: SCONFANAL SEARCHMETHOD=SYSTEMATIC REPRUNECONFS=11,15,0.75|
||SYSTEMATIC for smaller, less flexible systems.
MONTECARLO for larger more flexible systems.
|Set the maximum number of returned conformers to N. The program attempts to select the most diverse set representing the entire population within the energy||100|
|WINDOW=||Sets the maximum (delta) energy at which a trial conformer will be saved in the data set. Conformers with an energy greater than the current minimum energy plus this value are rejected.||10.0 (kcal/mol)|
|KEEPALL||Keep all generated conformations. This is similar to maximizing MAXCONFS and WINDOW options, but will also keep some conformers typically thrown away because of bond strain.|
|Maximum number of attempted molecules. Only meaningful for the MONTECARLO method. This is controlled from the "Maximum Conformers Controlled" entry in the setup panel.||A complicated function. see How many cycles...|
|MCCONFS=||The Monte Carlo algorithm will do this number of steps, overriding the "Maximum Steps" and the default count.|
||Changes the default 6-member ring move (cyclohexane) to attempt to find the twist-boat conformation. This dramatically slows down the algorithm as the number of possible moves changes from 2 to 27. If FINDBOATS is used the WINDOW= value is increased to 15 kcal/mol as twist-boat conformations are typically higher in energy (~6 kcal/mol for cyclohexane).||turned off by default|
|SKIPBOATS||Uses the fast cyclohexane move of correlated flips.||on by default|
|STARTTEMPERATURE=||The initial temperature for the monte carlo/simulated-annealing algorithm.||5000 K|
|NORIGID||Do not attempt to do any 'rigid moves' but rely on constraints to get the correct structure. This will likely slow down the algorithm.|
|NOOPT||Do only rigid moves and single points. Do not attempt to re-minimize. (Only useful for small "dynamic constraint" systems).|
|IGNORENOES||Ignore any NOE constraints in the system. The default is to use the NOE constraints as a filter only.|
|PASSNOES||Pass any NOE constraints on to the optimization engine. (Currently only supported by mechanics.) Thus all intermediate results satisfy the NOE constraints. The default is to use the NOE constraints as a filter.|
|NOEBIASE=||Used to bias the energy to favor conformations that satisfy the NOE constraints. By default this is turned off. Must be a positive number.||0.0 (kcal/mol)|
|SAVEINPROPARC||Instead of generating a new list of conformers save the conformers in the property archive for use in Spartan's database applications.|
|PRUNEMETHOD=i||Select a different algorithm when deciding which of the
conformers to be saved.
|Rerun the pruning algorithm as a property calculation. the optional i. i. tol are values for the PRUNEMETHOD=i, DISTANCEMEASURE=j, and DISTANCEISNEAR=tol keywords, respectively. This keyword is a 'property' keyword, and can only be used after a main conformation run which has been executed with the SAVEINPROPARC keyword.|
A scalar number used to measure distance between conformers.
|PRUNETOLERANCE=x||In the cluster pruning algorithms conformers are considered "near" if they are within this value. If this value is set to zero, this tolerance is not used, and the nearest pairs will be pruned until the number of conformers desired is reached. See DISTANCEMEASURE for the units and definition of distance used in these algorithms.||0.0|
|SPARSE=x||A modification of the systematic search, where a (random) subset of the systematic conformers are tried. If X > 1 then a total of X (random) conformers will be attempted. If X < 1 then a fraction (x) of the total conformers will be attempted.|
|CONF_SELECTION_RULE=i*||There are a number of default rules used to determine
which bonds to rotate.
These rules are split into different classes, each of
which is useful for different types of problems.
Rules used for all rule sets are:
|IGNORE_USERSELECTION||Ignore the bond selection from the user, and use the default rules for determining rotatable bonds. (User defaults are set whenever the user enters the 'set torsion' mode.)|
|DRYRUN||Execute only the setup part of conformational analysis. This is only used in debugging.|
|DISTANCEMEASURE=i||Measure to use in determining distance between two conformers.|
|CONFSEED=||The starting point for the random number generator.||different every time|
|keywords passed to underlying method|
|FREQ*||Will do a frequency calculation on the final candidates.|
|PRINTLEV=||Control Printing. See
Description of the output file for
PRINTLEV=2 displays a label for each conformation.
PRINTLEV=3 dumps the intermediate minimization output to the main output window
|...other keywords...||Unrecognized keywords will be passed to the underlying method. See below for some commonly used keywords.|
|Do dynamic constraints/Energy Profile.|
|SDYNCON||Do a energy profile but only return one result. (Usually, this result is a transition state, but if no local maxima exist the local minima will be returned.) This is not a recommended option, and is used primarily for debugging purposes.|
|DYNCONMETHOD=||If there are multiple
constraints how are these constraints applied
|KEEPSYMMETRY||Attempt to maintain the starting molecule's symmetry.|
|NORIGID||Do not attempt 'rigid moves' but rely on constraints to get the correct structure.|
|NOOPT||Do only rigid moves and single points. Do not attempt to re-minimize.|
|NOMECHPREOPT||Do not prefix each minimization with a mechanics constrained optimization. This is only meaningful for non-mechanic's methods such as AM1.|
|RIGIDONLY||Do only rigid moves and single points. Do not attempt to re-minimize. (Only useful for small "dynamic constraint" systems).|
|Save temporary files. Useful for debugging. SAVEFILES=2 (or greater) will save even more intermediate files including those of the sub-jobs.|
|NAMEPREF=abc||Save conformers (or energy profile steps) using the name 'abc'. (This will force the creation of a new file even if executing a 'Equilibrium Conformer' job.|
|* Keywords marked with an asterisk '*' should not be typed in. They are generated by the setup panel.|
|Keywords not recognized in the conformer/energy-profile module will be passed on the underlying method. Following are some keywords found to be useful.|
|Add the solvent model as a final perturbation. Thus, all minimizations are done with the base force field and a solvation 'correction' is applied to the final energy. SM50R is the most used mechanics solvation model. (POSTSOLVENT=SM50R)|
Last modified: Fri May 13 21:35:34 GMT 2016