Preparing the ligand: Difference between revisions

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*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will  convert your SMILES to ''isomeric'' SMILES.
*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will  convert your SMILES to ''isomeric'' SMILES.
*run <tt>dbgen.csh yourname.smi</tt>.   
*run <tt>dbgen.csh yourname.smi</tt>.   
*Note that the dbgen.csh does not work well for more that 1000 molecules.  Brake up your molecules into chunks of 1000 and run dbgen on each chunk.
*you should obtain a file <tt>somename.db.gz</tt> .
*you should obtain a file <tt>somename.db.gz</tt> .



Revision as of 20:50, 31 July 2012

Preparing a ligand

Automatic way, starting from SMILES

This way 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 convert.py --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 well for more that 1000 molecules. Brake up your molecules into chunks of 1000 and run dbgen on each chunk.
  • you should obtain a file somename.db.gz .

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 file2file.py 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!

file2file.py -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
(per_atom)


  • 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 .