First if you are going to position your molecule in the binding site of a protein and you want to include the electrostatics in the score you should add hydrogens and charges to your small molecule before doing anything else. If you are simply using the electron density for the score then it is not necessary to add hydrogens and charges. For a PDB file the charge should go in the column after the bfactor column.
If you want to position your molecule as a rigid body the PDB file for your molecule should be formatted as follows:
| ROOT N 0 |
| ... |
| atom records |
| ... |
| ENDMOLECULE |
where the atom records are standard PDB records. If you are only positioning a rigid molecule you can skip the rest of this section.
For those of you who are dealing with a flexible molecule the program Flexible will insert the necessary formatting information if it is given the necessary information. A standard MOL2 formatted file or an extended PDB formatted file should do the trick. An extended PDB formatted file looks like
| ATOM ..... |
| ATOM ..... |
| ... |
| ATOM ..... |
| BOND ..... |
| ... |
| BOND ..... |
| END |
The ATOM records are identical to those in the standard PDB formatted files. The BOND records contain the bond information in the form:
| BOND N1 N2 TYPE |
The record says that atom N1 is bonded to N2 by a bond of type TYPE. For example
| BOND 1 2 2 |
means that atoms 1 and 2 are double bonded. For the purposes of the program Flexible, bonds of type 1 are considered rotatable and bonds of any other type are considered not rotatable. Thus you need not worry about distinguishing between double and triple bonds. Rather worry about distinguishing between those bonds you want to be rotatable and those that you do not want to be rotatable. Rings are always treated as rigid. The same discussion goes for MOL2 files: the bond type is important only in that it distinguishes between rotatable and everything else.
All the programs with this package are interfaced through command line arguments. Typically if a program name is typed at the command line with the incorrect command line arguments then the result is an error message showing which arguments are required and which are optional. Often if you forget exactly how to use a program executing it at the command line will give you enough information to jar your memory. For example, entering Flexible will result in the error message:
| USAGE Flexible | -i[required] Input File |
| -o[required] Output File | |
| -f[required] Atom Format |
The -i option specifies the input file, the -o option specifies the output file (PDB format), and the -f option specifies the atom format for both input and output. The atom format will be discussed is section 8. The input file should be either extended PDB format (as described above) or in MOL2 format. The output file will be a PDB file with some additional flexibility information. The proper usage of Flexible is
| Flexible -i YYY.pdb -o ZZZ.pdb -f 0 |
The file YYY.pdb is the extended pdb file with the BOND records. The file ZZZ.pdb is the file that will be used by Blob.