Sat Oct 8 18:28:40 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 Sat Oct 8 2011 at 18:28:40 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! 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 501 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: 0.6284534 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 0.6284534 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2603 total number of charged atoms : 2487 net assigned charge : 4.500006 assigned positive charge : 397.2450 centred at (gu) : 88.47802 89.49575 89.89426 assigned negative charge : -392.7455 centred at (gu) : 88.37662 89.53294 89.78008 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 53678 no. pairs analyzed = 53678 no. exposed pairs = 3077 no. arc points = 21703 no. surface atoms = 1035 nbur = 1568 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3857 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.2000000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2103 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1919367E-09 1.4120966E-08 midg,1,midg; midg,igrid,midg 8.8966763E-09 1.4785814E-09 1,midg,midg; igrid,midg,midg -5.6723284E-09 9.6389892E-09 gauss-seidel spectral radius is 0.9868826 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 18:28:41 rms-change max change #iterations 0.1362566 24.33756 at 10iterations 1.2908594E-02 1.835953 at 20iterations 1.2389671E-03 0.1716995 at 30iterations 1.1837494E-04 1.6921997E-02 at 40iterations 1.1306967E-05 1.4514923E-03 at 50iterations finished qdiffx linear iterations at : 18:28:43 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.1306967E-05 1.4514923E-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) 3.380000 DelPhi exited at 18:28:44 3.383u 0.168s 0:03.87 91.4% 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 18:28:44 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! 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 501 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: 1.885360 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 1.885360 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2603 total number of charged atoms : 2487 net assigned charge : 4.500006 assigned positive charge : 397.2450 centred at (gu) : 85.43347 88.48696 89.68223 assigned negative charge : -392.7455 centred at (gu) : 85.12962 88.59863 89.33992 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 grid for indexing accessible points = 1.400000 m= 26537 mr = 51771 m= 3861 mr = 19864 m= 230 mr = 2445 m= 1 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4367 time to turn everything in is 0.3600000 number of dielectric boundary points 30136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19532 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) : 0.6284534 object centre at (A) : -7.086999 -0.7659998 16.12550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0503474E-02 3.4811269E-02 midg,1,midg; midg,igrid,midg 1.2960096E-02 -6.6720578E-04 1,midg,midg; igrid,midg,midg -3.0879837E-03 3.8276199E-02 gauss-seidel spectral radius is 0.9986049 estimated iterations to convergence 212 setup time was (sec) 0.5700000 now iterating at: 18:28:45 rms-change max change #iterations 4.153586 179.8076 at 10iterations 1.930206 61.37939 at 20iterations 0.8980506 28.64986 at 30iterations 0.4168569 14.79274 at 40iterations 0.1932892 6.008548 at 50iterations 9.0122387E-02 2.857010 at 60iterations 4.1788109E-02 1.304537 at 70iterations 1.9463716E-02 0.6269033 at 80iterations 9.0423087E-03 0.3030567 at 90iterations 4.2123711E-03 0.1312504 at 100iterations 1.9570827E-03 6.1447144E-02 at 110iterations 9.0909447E-04 2.7546883E-02 at 120iterations finished qdiffx linear iterations at : 18:28:52 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 9.0909447E-04 2.7546883E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 18:28:52 7.732u 0.207s 0:08.22 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 18:28:52 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! 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 501 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: 2.828040 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 2.828040 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2603 total number of charged atoms : 2487 net assigned charge : 4.500006 assigned positive charge : 397.2450 centred at (gu) : 83.15008 87.73048 89.52313 assigned negative charge : -392.7455 centred at (gu) : 82.69434 87.89784 89.00981 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 grid for indexing accessible points = 1.400000 m= 86699 mr = 124734 m= 30685 mr = 71795 m= 6893 mr = 25020 m= 972 mr = 5319 m= 58 mr = 703 m= 0 mr = 20 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 14265 time to turn everything in is 0.9200000 number of dielectric boundary points 67870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19894 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) : 1.885360 object centre at (A) : -7.086999 -0.7659998 16.12550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1459614 0.3896807 midg,1,midg; midg,igrid,midg 0.1558148 -3.7482124E-02 1,midg,midg; igrid,midg,midg 7.3992866E-03 0.4755560 gauss-seidel spectral radius is 0.9992449 estimated iterations to convergence 287 setup time was (sec) 1.150000 now iterating at: 18:28:54 rms-change max change #iterations 9.734044 334.6756 at 10iterations 5.608791 153.8988 at 20iterations 3.206474 66.49721 at 30iterations 1.836002 34.00694 at 40iterations 1.051773 19.02629 at 50iterations 0.5998726 12.41879 at 60iterations 0.3434613 6.583931 at 70iterations 0.1960590 3.484907 at 80iterations 0.1120493 1.956743 at 90iterations 6.3771605E-02 1.219282 at 100iterations 3.6479928E-02 0.6985092 at 110iterations 2.0781368E-02 0.3644924 at 120iterations 1.1907880E-02 0.2191181 at 130iterations 6.7892033E-03 0.1258430 at 140iterations 3.8754889E-03 6.8592072E-02 at 150iterations 2.2136229E-03 3.8375854E-02 at 160iterations 1.2612607E-03 2.3345947E-02 at 170iterations 7.2187628E-04 1.2446880E-02 at 180iterations finished qdiffx linear iterations at : 18:29:05 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 7.2187628E-04 1.2446880E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 18:29:05 12.508u 0.204s 0:13.02 97.5% 0+0k 0+0io 0pf+0w