QikProp Input Structures

QikProp input structures and files must meet the following criteria:

  • Structures must be three-dimensional, not two-dimensional.

  • Hydrogen atoms must be explicit. You cannot, therefore, use structures with united-atom types from molecular mechanics programs. If your input contains such structures, Maestro prompts you to correct the hydrogen treatment. There is no check for missing hydrogens when you run QikProp from the command line.

  • With the exception of $$$$-delimited MDL SD mol files and Maestro-formatted files, each structure file must contain only one molecule. You can concatenate MDL SD mol (jobname.mol) files into a single file for input to QikProp. For an example, see the file $SCHRODINGER/qikprop-vversion/molfiles/many.mol.

  • The allowed elements are H, C, N, O, F, Al, Si, P, S, Cl, Br, and I. In fast processing mode all atom types are permitted, though some results might not be valid if atoms other than the above PM3 atoms are used.

  • The number of atoms must not exceed 1000 atoms in the fast mode or 100 non-hydrogen and 150 hydrogen atoms in normal processing mode.

Charged input structures do not have to be neutralized prior to processing, because QikProp neutralizes them internally, and copies the QikProp properties for the neutral species to the original (charged) input structure for output to file. In normal mode, if QikProp is unable to neutralize a structure, such as in the case of a quarternary ammonium compound, that ligand is skipped and no properties are generated.

If your structures do not meet any of the above criteria, you can use LigPrep to preprocess the structures so that they are ready for input to QikProp. LigPrep converts structures from 2D to 3D, ensures that explicit hydrogen atoms are used and performs a molecular mechanics minimization. See the LigPrep User Manual — Contents for more information on using this product.

QikProp results are not very sensitive to the conformation of the input structure. Where there is variation of the results with conformation, extended structures generally give results that are closer to the experimental data than compact structures. QikProp results are also not very sensitive to the details of structure optimization, though some form of optimized structure should be used for the input. See Conformation Dependence of Results for more information.

QikProp processes some additional entries in standard MDL SD mol files, as follows. If there is an entry called <MOLNAME>, QikProp reads the following line for the molecule name that is written to all files. If there is an entry called <MDLNUMBER> or <MOLCODE>, this entry is written after the molecule name in the jobname.out file.