The sidechain degree of freedom is the most complex. There are presently six different ways of constructing sidechains. See Sidechain Overview, for more information about the sidechain degree of freedom.
Unlike the other degrees of freedom, many of the options are associated with particular residues. I.e., they are position dependent. These position dependent options are MAXEVDW, SGRID, VAVOID, CLUMP, and NOSYMMETRY. The program will first scan the command string for the first of these options, and it will use that value as the default for all the residues. Then, starting with this default, it will scan for options and residues (STARTRES and LASTRES options below). Each time it finds an option specification, the current value is changed. Each time it finds a residue, the option settings for that residue will be set to the current value.
The residues whose sidechains are to be constructed are specified with an arbitrary number of STARTRES and LASTRES commands. Each LASTRES command is paired with the previous STARTRES command, and all residues within the pair are constructed. However, a STARTRES command need not have a LASTRES pair, and in that case, only the residue specified in the STARTRES command will be processed. E.g., STARTRES H 30 STARTRES H 10 LASTRES H 12 STARTRES H 25 will search the sidechain conformational space for residues; H 10, H 11, H 12, H 25, and H 30. If not STARTRES command is given, then the residue specified in the last BACKBONE degree of freedom will be used.
The MAXEVDW option specifies the maximum repulsive contact for any atom within the sidechain. This option is position dependent as described above.
VAVOID and NOVAVOID control whether van der Waals repulsion avoidance is used. VAVOID signifies that avoidance is to be done. Van der Waals repulsion avoidance results in the program using only those torsion angles which avoid any van der Waals contact greater than MAXEVDW. Every atom that can make contact with the atoms in a clump are checked. Any sampling of the sidechain grid that falls into a repulsive range is moved to the closest torsion angle within an acceptable range.
SGRID controls the sampling grid. If a numeric value is specified, the value is taken for the grid in degrees. The first value for the torsion angle is taken from the global minimum of the torsion angle potential for the free atom and its antecedents. If there are multiple minima, then the smallest value in the range is taken. If MIN is specified, then the grid is set to the local minima in the energy of the free torsion angle of the clump. If SELECT is specified, then you can specify the torsion angle grid as a function of the number of free torsions in the sidechain. Each number or MIN keyword specifies the sidechain grid to use starting with sidechains with one clump on up. The last value applies to all the larger sidechains. The keyword, AUTO, is equivalent to “SELECT 10 30 30 60 60 MIN END”.
The CLUMP option allows the user to specify a subset of clumps for succeeding residues. This is useful when one wishes to search over only a portion of a sidechain or a portion of an arbitrary molecule. The syntax of this option is intended to provide a simple means for specifying a range of clumps. If the option, ALL, is used, then succeeding residues will include all clumps. If a single word is given, then only clumps named by that word will be included. If the colon form of the option is used, then only clumps which are sequentially between the two names in the sidechain topology file entry for the residues will be used. If a word is omitted on either side of the colon, then either the first or last clump of each residue will be used as the default, respectively. A solitary colon is thus the same as the ALL option. If you want to use disjoint subsets of clumps within one residue, simply specify two sets of CLUMP and STARTRES commands.
For example, suppose one wished to search over the gamma carbons and gamma 2 hydrogens of a valine alone. These are currently listed as clumps 1 and 3 in the valine residue in the sidechain topology file. Assume that the valine is in segment MAIN and has residue identifier 46. Then the following command segment would be appropriate:
SIDE CLUMP 1 STARTRES MAIN 46 - CLUMP 3 STARTRES MAIN 46 ...
SYMMETRY and NOSYMMETRY controls whether clump symmetry is used. Normally, the rotational symmetry associated with a clump (see Sidechain Topology), reduces the search space. However, the elimination of this symmetry is occasionally desirable because the comparison command of the analysis facility (see Comparisons) does not recognize symmetric elements in residues and can generate artifactually large differences. The effect of NOSYMMETRY is make all clumps have symmetry of 1.
SIDEOPT specifies the sidechain construction method. See Sidechain Degree of Freedom, for more details. The default is FIRST.
There is an important optimization which is performed when the FIRST sidechain construction method is used. (It is also important for the ITERATIVE method too, because this method uses a conformation generated by FIRST to get started.) If the FIRST method fails to find a conformation for a particular residue, it will backtrack in the set of residues being constructed to the first residue which made contact with the failed residue. If no such residue exists, then the search fails. In order to make this work in the optimal way, you should group residues whose sidechain interact together when specifying their order. In addition, the global option, NOSOPT, will turn off this optimization.
NCOMB specifies the number of combinations to be used for the COMBINATION method. The default is 2.
EVAL specifies how the sidechain conformations are to be evaluated when the ITERATIVE, INDEPENDENT, and COMBINATION options are used. For the RMS and WRMS options to work, the coordinates stored in the program prior to the execution of the CONGEN command must be the reference set. The WRMS option means Worst RMS.
MAXSIDEITER controls how many iterations over all the residue are performed during an iterative sidechain construction. The default is 10.