Sun Oct 9 07:24:02 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 Sun Oct 9 2011 at 07:24:02 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1571 !!! WARNING: HIT 45 has a net charge of 0.5140 !!! WARNING: SEP 63 has a net charge of -0.4750 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 102 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7639649 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): -6.549000 35.24800 ymin,ymax (A): -2.310000 39.95400 zmin,zma (A): -13.35600 33.24300 x,y,z range (A): 41.79700 42.26400 46.59900 scale (grids/A): 0.7639649 object centre (A): 14.34950 18.82200 9.943501 number of atom coordinates read : 1571 total number of charged atoms : 1426 net assigned charge : -9.029992 assigned positive charge : 230.2262 centred at (gu) : 90.56467 89.27151 90.91986 assigned negative charge : -239.2561 centred at (gu) : 90.37912 89.67225 91.00652 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6506 nv = 96 ne = 84 npr = 32102 no. pairs analyzed = 32102 no. exposed pairs = 2108 no. arc points = 15022 no. surface atoms = 717 nbur = 854 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 3529 m= 9 mr = 109 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1081 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3828297E-07 -4.3916287E-07 midg,1,midg; midg,igrid,midg 2.3697885E-07 -6.7689439E-07 1,midg,midg; igrid,midg,midg -4.4806578E-07 -4.6622880E-08 gauss-seidel spectral radius is 0.9910176 estimated iterations to convergence 86 setup time was (sec) 0.5900000 now iterating at: 07:24:02 rms-change max change #iterations 0.2467955 39.26370 at 10iterations 3.5047844E-02 5.335249 at 20iterations 4.9510645E-03 0.9313583 at 30iterations 7.0732000E-04 9.7114563E-02 at 40iterations 1.0126357E-04 1.5150070E-02 at 50iterations finished qdiffx linear iterations at : 07:24:06 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.0126357E-04 1.5150070E-02 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 07:24:06 4.233u 0.238s 0:04.74 94.0% 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 Sun Oct 9 2011 at 07:24:07 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1571 !!! WARNING: HIT 45 has a net charge of 0.5140 !!! WARNING: SEP 63 has a net charge of -0.4750 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 102 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.291895 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): -6.549000 35.24800 ymin,ymax (A): -2.310000 39.95400 zmin,zma (A): -13.35600 33.24300 x,y,z range (A): 41.79700 42.26400 46.59900 scale (grids/A): 2.291895 object centre (A): 14.34950 18.82200 9.943501 number of atom coordinates read : 1571 total number of charged atoms : 1426 net assigned charge : -9.029992 assigned positive charge : 230.2262 centred at (gu) : 91.69401 87.81491 92.75977 assigned negative charge : -239.2561 centred at (gu) : 91.13741 89.01665 93.01971 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 67212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15022 grid for indexing accessible points = 1.400000 m= 28370 mr = 45109 m= 6653 mr = 21950 m= 732 mr = 4665 m= 27 mr = 450 m= 1 mr = 4 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 30818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 11371 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) : 0.7639649 object centre at (A) : 14.34950 18.82200 9.943501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6613449E-03 -6.1483499E-02 midg,1,midg; midg,igrid,midg 1.3116134E-02 -0.1185164 1,midg,midg; igrid,midg,midg -8.0818735E-02 -2.7045611E-02 gauss-seidel spectral radius is 0.9989406 estimated iterations to convergence 243 setup time was (sec) 1.050000 now iterating at: 07:24:08 rms-change max change #iterations 4.672172 201.8581 at 10iterations 2.396202 100.8992 at 20iterations 1.223153 36.69736 at 30iterations 0.6294213 20.15002 at 40iterations 0.3225670 9.286333 at 50iterations 0.1654370 5.407104 at 60iterations 8.5003451E-02 2.518588 at 70iterations 4.3585349E-02 1.427048 at 80iterations 2.2330694E-02 0.7108941 at 90iterations 1.1465040E-02 0.3600345 at 100iterations 5.8538085E-03 0.1807513 at 110iterations 2.9971437E-03 8.8463306E-02 at 120iterations finished qdiffx linear iterations at : 07:24:16 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 2.9971437E-03 8.8463306E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 07:24:17 9.737u 0.265s 0:10.27 97.2% 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 Sun Oct 9 2011 at 07:24:17 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1571 !!! WARNING: HIT 45 has a net charge of 0.5140 !!! WARNING: SEP 63 has a net charge of -0.4750 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 102 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.437842 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): -6.549000 35.24800 ymin,ymax (A): -2.310000 39.95400 zmin,zma (A): -13.35600 33.24300 x,y,z range (A): 41.79700 42.26400 46.59900 scale (grids/A): 3.437842 object centre (A): 14.34950 18.82200 9.943501 number of atom coordinates read : 1571 total number of charged atoms : 1426 net assigned charge : -9.029992 assigned positive charge : 230.2262 centred at (gu) : 92.54114 86.72233 94.13972 assigned negative charge : -239.2561 centred at (gu) : 91.70615 88.52510 94.52959 start vw surface at 0.1500000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 154296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15022 grid for indexing accessible points = 1.400000 m= 84025 mr = 108669 m= 39253 mr = 69701 m= 12954 mr = 33163 m= 3051 mr = 10462 m= 444 mr = 2328 m= 34 mr = 322 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.200000 number of dielectric boundary points 69394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 11408 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) : 2.291895 object centre at (A) : 14.34950 18.82200 9.943501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8939821E-02 -0.9619042 midg,1,midg; midg,igrid,midg 0.1968675 -0.7128746 1,midg,midg; igrid,midg,midg -0.4926326 -0.1302201 gauss-seidel spectral radius is 0.9993276 estimated iterations to convergence 304 setup time was (sec) 2.600000 now iterating at: 07:24:20 rms-change max change #iterations 10.11820 289.1358 at 10iterations 6.026845 135.6882 at 20iterations 3.589602 72.49155 at 30iterations 2.133820 40.38846 at 40iterations 1.267723 24.28227 at 50iterations 0.7482830 12.75521 at 60iterations 0.4425460 8.007614 at 70iterations 0.2623151 5.565680 at 80iterations 0.1546438 2.770568 at 90iterations 9.1524944E-02 1.754286 at 100iterations 5.4074254E-02 1.033067 at 110iterations 3.1779807E-02 0.6217861 at 120iterations 1.8803129E-02 0.3149557 at 130iterations 1.1085891E-02 0.1849983 at 140iterations 6.5381085E-03 0.1244793 at 150iterations 3.8660110E-03 6.4146996E-02 at 160iterations 2.2817482E-03 3.8238049E-02 at 170iterations 1.3460520E-03 2.3808241E-02 at 180iterations finished qdiffx linear iterations at : 07:24:33 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 1.3460520E-03 2.3808241E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 07:24:34 16.334u 0.289s 0:16.90 98.2% 0+0k 0+0io 0pf+0w