Preparing the ligand

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Preparing a ligand

Automatic way, starting from SMILES

This way, you will make use of John's automatic scripts for database preparation and actually upload new molecules to a special section of ZINC.

  • it is advisable to create a special subdirectory, since many new files will be generated.
  • the file containing the SMILES strings should contain a string followed by an identifier on each line.
  • OPTIONAL: run --i=yourname.smi --o=yourname.ism . This will convert your SMILES to isomeric SMILES.
  • run dbgen.csh yourname.smi.
    • Note that the dbgen.csh does not work for more that 1000 molecules.
    • Brake up your molecules into chunks of 1000 and run dbgen on each chunk.
    • Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.
  • you should obtain a file somename.db.gz .


To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.

  • At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.
      • SetMaxConfs(600) #set to higher numbers ie. 1000
      • SetRMSThreshold(0.80) #set to lower numbers ie. 0.50
      • SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules
  • WARNING this should only be done if generating conformations for a small set of compounds!!!

Manual way

Isolating the ligand as .mol2 file

  • extract the ligand structure from the .pdb file.
  • assign hydrogens.
  • assign all atom (Sybyl/TAFF) and bond types.
  • save it as ligandname.mol2 file.

Running omega

  • run OMEGA, but don't ask me how to do that yet.

Running amsol

  • find more information about amsol on its homepage.
  • mkdir ./amsol2
  • Use to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original .mol2 file will be overwritten! -g ligandname.mol2 ./amsol2/someothername.mol2

  • edit ./amsol2/someothername.mol2 :
  • delete all lines prior to @<TRIPOS>MOLECULE
  • change line 2 (molecule name) to something of the format ABCD12345678 (four capital letters followed by eight numbers).
  • line 3 should be natoms nbonds 0 0 0
  • the @<TRIPOS>MOLECULE section must consist of exactly 5 lines (adjust by adding/deleting blanks).
  • remove all sections after the @<TRIPOS>BOND section.
  • delete the blank lines between the ATOM and BOND sections, if there are any.
  • run RunAMSOL3.csh WAIT
  • the output someothername.solv file will contain the following:
AMSOL output
line #1 molname <math>n_{atoms}</math> charge pol_solv  ? apol_solv total_solv
other lines charge pol_solv  ? apol_solv total_solv

  • furthermore, there will be someothername.nmol2 file which contains the correct partial charges.

Running mol2db

  • edit someothername.nmol2 so that the @<TRIPOS>MOLECULE section consists of exactly 6 lines.
  • edit the inhier file so that the 'mol2_file', 'db_file' and 'solvation_table' entries are correct.
  • run mol2db inhier
  • add the preamble at the top of the file.
  • gzip the resulting file so that it can be used by DOCK .