[Dock-fans] Multiple ligands

Gustavo HMF Souza desouz at fcm.unicamp.br
Tue Oct 3 20:27:16 PDT 2006

Hi all!


After running dock many times with one ligand and one receptor, I want to
know if is possible to construct a ligand database (with 50 different
ligands for example) and run all with the same receptor. So, 


First: How can I generate a ligand datafile set (with 50 different possible
ligands i.e. ?) May I have to concatenate all *.mol2 files (with previously
add hydrogens and ANTECHAMBER  AM1-BCC charge method only) OR
*flex_scored.mol2 ./dock run files? Can I use the following command:  cat
*.mol2 > ligand_database.mol2 to concatenate?


Second: How can I configure an *.in file to run with ./dock -i -o? (And
configure de same file to generate a dock ranking?);


Third: After all of this, how can I calculate a Ki constant for each one of
them? (This, assuming that all calculations is o.k. and I have a previous
pre-computed receptor grid.nrg ready to ./dock).


Be happy we are dock FANS!


Best regards!

Gustavo HMF Souza




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