Enabling DOCK Developer Scripts incl Database Preparation
Intel/Linux
inactives
we got past inactivesDB.ism
actives
we got past actives.ism
node-6-13.c.bkslab.org
du2 starts
1 molecule processed, 0 errors
first try already in
then inzinc
count is 0
bzcat: Can't open input file 51: No such file or directory.
bzcat: Can't open input file 02: No such file or directory.

convert.py (Tripos MOL2 -> MDL SDF):
	mols in: 1	mols out: 1

Total: 1 mols processed.
count is 0
bzcat: Can't open input file 25: No such file or directory.
bzcat: Can't open input file 89: No such file or directory.

convert.py (Tripos MOL2 -> MDL SDF):
	mols in: 1	mols out: 1

Total: 1 mols processed.
bzcat: Can't open input file 51: No such file or directory.
bzcat: Can't open input file 02: No such file or directory.
bzcat: Can't open input file 25: No such file or directory.
bzcat: Can't open input file 89: No such file or directory.
du2.csh script updated
ligand processing
MakeDOCK 2.0, modified by J.Irwin and M.Mysinger.
Previous versions by D.M.Lorber, B.Q.Wei, A.N.Kirschner, and N.Huang
Using scripts in /raid5/people/mysinger/xyz/dockenv.
Creating binding-site residue list
Creating molecular surface

rec.site is missing or zero size
there is probably an error in xtal-lig.pdb or rec.pdb
make: *** [rec.ms] Error 1
Grid preparation completed normally.
PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist.
 File name = ../grids/rec+sph.phi                                                            
 In source file scoreopt_so.f, at line number 140
PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist.
 File name = ../grids/vdw.parms.amb.mindock                                                  
 In source file scoreopt_so.f, at line number 198
PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist.
 File name = ../grids/rec+sph.phi                                                            
 In source file scoreopt_so.f, at line number 140
PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist.
 File name = ../grids/vdw.parms.amb.mindock                                                  
 In source file scoreopt_so.f, at line number 198
PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist.
 File name = ../grids/rec+sph.phi                                                            
 In source file scoreopt_so.f, at line number 140
PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist.
 File name = ../grids/vdw.parms.amb.mindock                                                  
 In source file scoreopt_so.f, at line number 198
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
going into second inactives test
after second inactives finished
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory
Permission denied, please try again.
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory
Permission denied, please try again.
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory
Permission denied (publickey,gssapi-with-mic,password).
                             FILTER PROGRAM

           THIS PROGRAM FILTERS ATOMIC COORDINATE FILES
             BASED ON DISTANCE AND SEQUENCE CRITERIA


name of file to filter by -
 xtal-lig.pdb                                                                    
 filter by atom names or numbers in receptor(na/nu)?
 residue/ligand orientation number increment filter?
  -100000
 Filter for MS run?(Y/N)
 N                                                                               
 Either names or numbers of the atoms to filter by, as 
 they appear in the pdb, with boolean and/or operators 
 if such apply between them.  Maximum of one boolean 
 per two filter atoms.
 name of ligand file-
 rec.pdb                                                                         
 names of ligand atoms to match against receptor 
 filters.  Include boolean and/ors between EACH 
 atom specified.
 LIGAND ATOM           1ISALL 
 internal filtering?
Y  
 distance cutoffs for each of the receptor atoms         specified-
    25.00000    
 output filename-
 poc.txt                                                                         
 number of allowed ligand contacts in an all-filter?
 LIGBUM IS-           0
 IR IS          67
 Number of atoms in ligand -            0
 IL IS           0
 NR IS-           1
 INTERNAL BEGUN
 INTERNAL COMPLETED
            1
 NUMLIG IS-           1
 TOTAL NUMBER OF ORIENTATIONS WRITEN IS -           0
 filtering complete
mf7.csh  - site preparation complete, preliminary docking queued