Sat Oct 8 21:01:24 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 Sat Oct 8 2011 at 21:01:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 506 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6138248 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): -10.56100 39.08900 ymin,ymax (A): -22.39900 24.73900 zmin,zma (A): -12.60600 45.39100 x,y,z range (A): 49.65000 47.13800 57.99700 scale (grids/A): 0.6138248 object centre (A): 14.26400 1.170000 16.39250 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.000008 assigned positive charge : 392.5590 centred at (gu) : 88.50219 89.51558 89.65945 assigned negative charge : -388.5595 centred at (gu) : 88.37457 89.56108 89.54387 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6350 nv = 96 ne = 84 npr = 54561 no. pairs analyzed = 54561 no. exposed pairs = 2986 no. arc points = 21275 no. surface atoms = 1005 nbur = 1597 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3552 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.2000000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7940 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9978363E-09 8.4449336E-09 midg,1,midg; midg,igrid,midg 5.9001479E-09 2.4854488E-10 1,midg,midg; igrid,midg,midg -6.2321543E-09 7.0062023E-09 gauss-seidel spectral radius is 0.9862518 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 21:01:25 rms-change max change #iterations 0.1234051 18.39447 at 10iterations 1.1077872E-02 1.701874 at 20iterations 9.9150476E-04 0.1612625 at 30iterations 8.9730725E-05 1.2458801E-02 at 40iterations 7.9461315E-06 1.2130737E-03 at 50iterations finished qdiffx linear iterations at : 21:01:28 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 7.9461315E-06 1.2130737E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 21:01:28 3.537u 0.182s 0:03.99 92.9% 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 Sat Oct 8 2011 at 21:01:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 506 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.841475 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): -10.56100 39.08900 ymin,ymax (A): -22.39900 24.73900 zmin,zma (A): -12.60600 45.39100 x,y,z range (A): 49.65000 47.13800 57.99700 scale (grids/A): 1.841475 object centre (A): 14.26400 1.170000 16.39250 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.000008 assigned positive charge : 392.5590 centred at (gu) : 85.50635 88.54612 88.97797 assigned negative charge : -388.5595 centred at (gu) : 85.12359 88.68309 88.63144 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21275 grid for indexing accessible points = 1.400000 m= 23472 mr = 48739 m= 3082 mr = 17237 m= 121 mr = 1823 m= 0 mr = 44 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5173 time to turn everything in is 0.3300000 number of dielectric boundary points 28085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19295 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) : 0.6138248 object centre at (A) : 14.26400 1.170000 16.39250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4738942E-02 2.0772576E-02 midg,1,midg; midg,igrid,midg 1.3664689E-02 2.7823241E-03 1,midg,midg; igrid,midg,midg -8.5124625E-03 3.7395101E-02 gauss-seidel spectral radius is 0.9985361 estimated iterations to convergence 207 setup time was (sec) 0.5400000 now iterating at: 21:01:29 rms-change max change #iterations 3.924536 169.8089 at 10iterations 1.787475 63.22761 at 20iterations 0.8128216 28.56956 at 30iterations 0.3712624 12.09857 at 40iterations 0.1694638 6.030153 at 50iterations 7.7412538E-02 2.673162 at 60iterations 3.5318758E-02 1.120084 at 70iterations 1.6114071E-02 0.5026741 at 80iterations 7.3171281E-03 0.2519073 at 90iterations 3.3556332E-03 0.1171637 at 100iterations 1.5294602E-03 4.8233032E-02 at 110iterations 6.9749879E-04 2.2603989E-02 at 120iterations finished qdiffx linear iterations at : 21:01:36 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 6.9749879E-04 2.2603989E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 21:01:37 7.946u 0.225s 0:08.46 96.4% 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 Sat Oct 8 2011 at 21:01:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 506 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.762212 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): -10.56100 39.08900 ymin,ymax (A): -22.39900 24.73900 zmin,zma (A): -12.60600 45.39100 x,y,z range (A): 49.65000 47.13800 57.99700 scale (grids/A): 2.762212 object centre (A): 14.26400 1.170000 16.39250 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.000008 assigned positive charge : 392.5590 centred at (gu) : 83.25954 87.81909 88.46677 assigned negative charge : -388.5595 centred at (gu) : 82.68536 88.02454 87.94713 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 160635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21275 grid for indexing accessible points = 1.400000 m= 78359 mr = 117912 m= 25347 mr = 64382 m= 5244 mr = 20232 m= 575 mr = 3861 m= 33 mr = 383 m= 0 mr = 18 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 17483 time to turn everything in is 0.8800000 number of dielectric boundary points 63405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19687 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) : 1.841475 object centre at (A) : 14.26400 1.170000 16.39250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1677857E-02 0.2203871 midg,1,midg; midg,igrid,midg 0.1528964 3.1918854E-02 1,midg,midg; igrid,midg,midg -7.7633515E-02 0.5340478 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.130000 now iterating at: 21:01:38 rms-change max change #iterations 9.281264 279.8494 at 10iterations 5.302036 117.5393 at 20iterations 3.011246 58.54804 at 30iterations 1.709875 34.60696 at 40iterations 0.9689044 18.89169 at 50iterations 0.5507495 10.49679 at 60iterations 0.3115221 5.918144 at 70iterations 0.1763086 3.624632 at 80iterations 9.9930704E-02 2.099594 at 90iterations 5.6672815E-02 1.075854 at 100iterations 3.2112479E-02 0.6460190 at 110iterations 1.8198293E-02 0.3449392 at 120iterations 1.0272892E-02 0.1994228 at 130iterations 5.8353445E-03 0.1078091 at 140iterations 3.3000980E-03 6.5088272E-02 at 150iterations 1.8696242E-03 3.4812927E-02 at 160iterations 1.0584171E-03 1.9725800E-02 at 170iterations 6.0043973E-04 1.1247635E-02 at 180iterations finished qdiffx linear iterations at : 21:01:50 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 6.0043973E-04 1.1247635E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 21:01:50 13.234u 0.250s 0:13.83 97.4% 0+0k 0+0io 0pf+0w