Mon Oct 10 14:03:37 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+sph.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 = amb.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 Mon Oct 10 2011 at 14:03:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 0.6442972 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): -11.54600 39.35300 ymin,ymax (A): -23.57800 24.12900 zmin,zma (A): 0.6279999 55.88200 x,y,z range (A): 50.89899 47.70700 55.25400 scale (grids/A): 0.6442972 object centre (A): 13.90350 0.2754993 28.25500 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 5.500008 assigned positive charge : 394.9646 centred at (gu) : 89.98678 90.03885 90.66357 assigned negative charge : -389.4654 centred at (gu) : 89.92220 89.90029 90.73005 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7133 nv = 96 ne = 84 npr = 50415 no. pairs analyzed = 50415 no. exposed pairs = 3310 no. arc points = 23377 no. surface atoms = 1098 nbur = 1461 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3795 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3600000 number of dielectric boundary points 3703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8542 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5491638E-08 2.8995531E-10 midg,1,midg; midg,igrid,midg -9.2855474E-09 2.7304335E-08 1,midg,midg; igrid,midg,midg 5.7802957E-10 1.7513159E-08 gauss-seidel spectral radius is 0.9875162 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 14:03:39 rms-change max change #iterations 0.1445859 23.09187 at 10iterations 1.4944499E-02 2.120320 at 20iterations 1.6760100E-03 0.2744064 at 30iterations 2.5464103E-04 3.8879395E-02 at 40iterations 5.7726065E-05 8.3847046E-03 at 50iterations finished qdiffx linear iterations at : 14:03:41 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.7726065E-05 8.3847046E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 14:03:42 3.490u 0.150s 0:04.40 82.7% 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 Mon Oct 10 2011 at 14:03:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.932892 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): -11.54600 39.35300 ymin,ymax (A): -23.57800 24.12900 zmin,zma (A): 0.6279999 55.88200 x,y,z range (A): 50.89899 47.70700 55.25400 scale (grids/A): 1.932892 object centre (A): 13.90350 0.2754993 28.25500 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 5.500008 assigned positive charge : 394.9646 centred at (gu) : 89.95957 90.11576 91.99000 assigned negative charge : -389.4654 centred at (gu) : 89.76623 89.70070 92.18977 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23377 grid for indexing accessible points = 1.400000 m= 27018 mr = 51765 m= 4271 mr = 19325 m= 296 mr = 2468 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.6300000 number of dielectric boundary points 34140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19025 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) : 0.6442972 object centre at (A) : 13.90350 0.2754993 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8553272E-02 4.9247127E-03 midg,1,midg; midg,igrid,midg -9.5545156E-03 1.8563112E-02 1,midg,midg; igrid,midg,midg 8.3784442E-03 6.3778558E-03 gauss-seidel spectral radius is 0.9986781 estimated iterations to convergence 218 setup time was (sec) 0.9200000 now iterating at: 14:03:43 rms-change max change #iterations 4.376931 185.1785 at 10iterations 2.070615 77.02402 at 20iterations 0.9785594 29.03405 at 30iterations 0.4620787 13.65718 at 40iterations 0.2198559 7.058976 at 50iterations 0.1043950 3.379776 at 60iterations 4.9315199E-02 1.536198 at 70iterations 2.3413451E-02 0.7439489 at 80iterations 1.1172912E-02 0.3965049 at 90iterations 5.3019384E-03 0.1617432 at 100iterations 2.5406275E-03 8.0075264E-02 at 110iterations 1.2234439E-03 4.1053772E-02 at 120iterations finished qdiffx linear iterations at : 14:03:50 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 1.2234439E-03 4.1053772E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 14:03:50 7.578u 0.190s 0:08.26 93.9% 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 Mon Oct 10 2011 at 14:03:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 2.899338 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): -11.54600 39.35300 ymin,ymax (A): -23.57800 24.12900 zmin,zma (A): 0.6279999 55.88200 x,y,z range (A): 50.89899 47.70700 55.25400 scale (grids/A): 2.899338 object centre (A): 13.90350 0.2754993 28.25500 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 5.500008 assigned positive charge : 394.9646 centred at (gu) : 89.93929 90.17342 92.98484 assigned negative charge : -389.4654 centred at (gu) : 89.64921 89.55089 93.28463 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 176038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23377 grid for indexing accessible points = 1.400000 m= 88033 mr = 125718 m= 30844 mr = 70756 m= 7364 mr = 24053 m= 1234 mr = 5159 m= 89 mr = 810 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 5660 time to turn everything in is 1.570000 number of dielectric boundary points 77072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19328 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) : 1.932892 object centre at (A) : 13.90350 0.2754993 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1880894 -7.7255659E-02 midg,1,midg; midg,igrid,midg -0.1612210 0.2099736 1,midg,midg; igrid,midg,midg 0.1735293 -4.9861264E-03 gauss-seidel spectral radius is 0.9992705 estimated iterations to convergence 292 setup time was (sec) 1.900000 now iterating at: 14:03:53 rms-change max change #iterations 10.35630 430.2871 at 10iterations 6.151772 154.3809 at 20iterations 3.609553 76.11148 at 30iterations 2.121563 42.76306 at 40iterations 1.239212 25.09998 at 50iterations 0.7210146 12.83391 at 60iterations 0.4203275 7.863121 at 70iterations 0.2442713 4.823090 at 80iterations 0.1416527 2.873154 at 90iterations 8.2032934E-02 1.454403 at 100iterations 4.7511838E-02 0.8460932 at 110iterations 2.7535483E-02 0.5518570 at 120iterations 1.5988166E-02 0.3112392 at 130iterations 9.3034860E-03 0.1667373 at 140iterations 5.4541496E-03 9.7105026E-02 at 150iterations 3.2243202E-03 5.6022167E-02 at 160iterations 1.9401140E-03 3.5007477E-02 at 170iterations 1.1952595E-03 2.4307251E-02 at 180iterations finished qdiffx linear iterations at : 14:04:04 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.1952595E-03 2.4307251E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 14:04:04 13.259u 0.231s 0:13.95 96.6% 0+0k 0+0io 0pf+0w