Preparing the ligand: Difference between revisions

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*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].   
*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].   
*<tt>mkdir ./amsol2</tt>   
*<tt>mkdir ./amsol2</tt>   
*<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt>  Uses file2file.py to get the right formal charge for AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!
Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!
*<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt>     
*edit <tt>./amsol2/someothername.mol2</tt> :     
*edit <tt>./amsol2/someothername.mol2</tt> :     
*
*

Revision as of 22:26, 18 March 2009

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.
  • 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

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 .