Tue Oct 11 08:29:15 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:29:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: HIR 85 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: GLU 295 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6368971 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -5.708000 50.18800 ymin,ymax (A): 9.472000 62.04300 zmin,zma (A): 0.6320001 55.50400 x,y,z range (A): 55.89600 52.57100 54.87200 scale (grids/A): 0.6368971 object centre (A): 22.24000 35.75750 28.06800 number of atom coordinates read : 2838 total number of charged atoms : 2627 net assigned charge : 4.039016 assigned positive charge : 424.2488 centred at (gu) : 89.97742 90.22109 91.07124 assigned negative charge : -420.2102 centred at (gu) : 90.16206 90.14328 91.00255 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7294 nv = 96 ne = 84 npr = 59924 no. pairs analyzed = 59924 no. exposed pairs = 3313 no. arc points = 23016 no. surface atoms = 1125 nbur = 1713 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 4074 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2300 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1227806E-09 1.6611768E-08 midg,1,midg; midg,igrid,midg -3.6289787E-09 1.4915329E-08 1,midg,midg; igrid,midg,midg 2.6386784E-08 -1.6488089E-08 gauss-seidel spectral radius is 0.9872405 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 08:29:16 rms-change max change #iterations 0.1536037 21.39706 at 10iterations 1.5231367E-02 2.682343 at 20iterations 1.5026263E-03 0.2225380 at 30iterations 1.5574424E-04 2.3155212E-02 at 40iterations 1.6495771E-05 2.1781921E-03 at 50iterations finished qdiffx linear iterations at : 08:29:18 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.6495771E-05 2.1781921E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 08:29:19 3.094u 0.136s 0:03.66 87.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:29:19 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: HIR 85 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: GLU 295 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.910691 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -5.708000 50.18800 ymin,ymax (A): 9.472000 62.04300 zmin,zma (A): 0.6320001 55.50400 x,y,z range (A): 55.89600 52.57100 54.87200 scale (grids/A): 1.910691 object centre (A): 22.24000 35.75750 28.06800 number of atom coordinates read : 2838 total number of charged atoms : 2627 net assigned charge : 4.039016 assigned positive charge : 424.2488 centred at (gu) : 89.93179 90.66244 93.21317 assigned negative charge : -420.2102 centred at (gu) : 90.48585 90.42953 93.00734 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23016 grid for indexing accessible points = 1.400000 m= 29252 mr = 53801 m= 5104 mr = 21896 m= 302 mr = 3229 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 301 time to turn everything in is 0.5600000 number of dielectric boundary points 33224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20701 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6368971 object centre at (A) : 22.24000 35.75750 28.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0528050E-02 8.1844255E-02 midg,1,midg; midg,igrid,midg -4.9724709E-03 -3.6192923E-03 1,midg,midg; igrid,midg,midg 6.8279140E-02 -6.6344857E-02 gauss-seidel spectral radius is 0.9986618 estimated iterations to convergence 217 setup time was (sec) 0.8200000 now iterating at: 08:29:20 rms-change max change #iterations 4.493898 183.7348 at 10iterations 2.128114 74.87384 at 20iterations 0.9989942 29.57837 at 30iterations 0.4741408 14.26498 at 40iterations 0.2241965 6.818603 at 50iterations 0.1062546 3.137741 at 60iterations 5.0140046E-02 1.528621 at 70iterations 2.3659982E-02 0.7381401 at 80iterations 1.1164796E-02 0.3648357 at 90iterations 5.2713463E-03 0.1514301 at 100iterations 2.4976633E-03 9.3832970E-02 at 110iterations 1.1860466E-03 3.7824631E-02 at 120iterations finished qdiffx linear iterations at : 08:29:25 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 1.1860466E-03 3.7824631E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 08:29:26 6.897u 0.163s 0:07.37 95.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:29:26 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: HIR 85 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: GLU 295 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.866037 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -5.708000 50.18800 ymin,ymax (A): 9.472000 62.04300 zmin,zma (A): 0.6320001 55.50400 x,y,z range (A): 55.89600 52.57100 54.87200 scale (grids/A): 2.866037 object centre (A): 22.24000 35.75750 28.06800 number of atom coordinates read : 2838 total number of charged atoms : 2627 net assigned charge : 4.039016 assigned positive charge : 424.2488 centred at (gu) : 89.89764 90.99370 94.81966 assigned negative charge : -420.2102 centred at (gu) : 90.72861 90.64427 94.51088 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 179130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23016 grid for indexing accessible points = 1.400000 m= 92314 mr = 130132 m= 36362 mr = 75944 m= 9347 mr = 29673 m= 1298 mr = 7006 m= 62 mr = 826 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1059 time to turn everything in is 1.470000 number of dielectric boundary points 74918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 21016 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.910691 object centre at (A) : 22.24000 35.75750 28.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2478452 1.180774 midg,1,midg; midg,igrid,midg -2.4262702E-02 -0.2009802 1,midg,midg; igrid,midg,midg 1.255048 -0.8505620 gauss-seidel spectral radius is 0.9992638 estimated iterations to convergence 291 setup time was (sec) 1.740000 now iterating at: 08:29:28 rms-change max change #iterations 10.44767 385.8240 at 10iterations 6.113246 183.4481 at 20iterations 3.543591 83.79816 at 30iterations 2.060532 43.41333 at 40iterations 1.192919 22.42909 at 50iterations 0.6909050 11.97454 at 60iterations 0.3996173 6.911498 at 70iterations 0.2307749 4.099985 at 80iterations 0.1333354 2.546885 at 90iterations 7.6939277E-02 1.334856 at 100iterations 4.4349357E-02 0.7774048 at 110iterations 2.5567802E-02 0.4757280 at 120iterations 1.4748096E-02 0.2594080 at 130iterations 8.4930230E-03 0.1441293 at 140iterations 4.9096905E-03 8.8672638E-02 at 150iterations 2.8404635E-03 4.8461914E-02 at 160iterations 1.6467390E-03 2.7686119E-02 at 170iterations 9.6551928E-04 1.6571045E-02 at 180iterations finished qdiffx linear iterations at : 08:29:37 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 9.6551928E-04 1.6571045E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 08:29:38 11.290u 0.186s 0:11.77 97.4% 0+0k 0+0io 0pf+0w