automolprep.readme

最经典的分子对结软件

README FILE FOR:  AutoMolPrep.perl

   Jim Arnold: (Kuntz Group, Dept. of Pharm. Chem., UCSF)


PURPOSE OF PROGRAM:

   It prepares a list of molecules for docking, as below:


                            Separate Molecules, add Hydrogens and Charges to .mol2
                     _         file_rec.pdb/mol2, file_lig.pdb/mol2, 
                     /|        file_wat.pdb/mol2, file_met.pdb/mol2, 
                    /
  (list of) file.pdb --->   Connolly Surface, All Spheres, and Docking Sphere Set.
                    \          file_rec.ms, file_rec.sph, file_rec_as.sph (dock sph), 
                     \|
                     -      Grid Box and Docking Grids.
                               file_rec_box.pdb (grid box), file_rec_grid.bmp/cnt/nrg


NOTES:    

   - The program was written to simplify preparation for Docking to a large number 
     of proteins, and to make Dock easier to use.  

   - This program (or subroutines) can easily be called from an interface.


USE:

   "AutoMolDockPrep.perl protein.in <ret>"
           

CAVEAT:

   If a given crystal structure contains multiple copies of the protein/comples, 
   you must currently generate a new file that has only one copy of the complex
   before running AutoMolPrep.perl on that complex - otherwise SPHGEN will dump core.


EXAMPLE INPUT FILE: (protein.in):

   ##########################################
   # Protein input file to AutoMolPrep.perl
   #    format:  filename  central_residue
   ##########################################

   1tps.pdb     195
   1ca0.pdb     195
   1fle.pdb     195
   4phv.pdb      25
   etc...