- To keep the ligand's input position the same as in the ligand PDBQT, use the same “tran0” x,y,z values as those specified in the “about” line of the DPF.
- To keep the ligand's input orientation, use “quaternion0 1. 0. 0. 0.”.
- To keep the input conformation, use “dihe0” with a “0.” value for every torsion in the ligand.
- Note that, if you wish to keep some torsional(s) INACTIVE, you need to prepare the ligand in a special way, that is, it is not enough to edit the HEADER lines in the .pdbqt because these are not parsed by the program:
prepare_ligand4.py -l filename
Description of command... -l ligand_filename
//**Optional parameters:**// [-v] verbose output [-o pdbqt_filename] (output filename) [-d] dictionary to write types list and number of active torsions [-A] type(s) of repairs to make: bonds_hydrogens, bonds, hydrogens [-C] do not add charges [-p] preserve input charges on atom type, eg -p Zn [-U] cleanup type: nphs_lps, nphs, lps, '' [-B] type(s) of bonds to allow to rotate [-R] index for root [-F] check for and use largest non-bonded fragment (False) [-M] interactive (default is automatic) [-I] string of bonds to inactivate composed of zero-based atom indices eg 5_13_2_10 will inactivate atoms-atoms bond and atoms-atoms bond (default is '') [-Z] inactivate all active torsions (default is leave active)
Problem is that only ADT will write this type of file correctly for you as it changes the atom numbering relative to the original .pdb file.
Beware of the dihedral definition(s) if you use other method(s)!
To proceed in ADT 4.2: Ligand > Torsion Tree > Choose torsions … > Save .pdbqt