Enabling DOCK Developer Scripts incl Database Preparation
Intel/Linux
inactives
we got past inactivesDB.ism
actives
we got past actives.ism
node-6-07.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 68: No such file or directory.
bzcat: Can't open input file 66: No such file or directory.

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

Total: 1 mols processed.
count is 0
nothing to compress
bzcat: Can't open input file 68: No such file or directory.
bzcat: Can't open input file 66: No such file or directory.
nothing to compress
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
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
not ready
slept 360 waiting for decoys
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          68
 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