Tue Nov 22 14:09:36 PST 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 Tue Nov 22 2011 at 14:09:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6554238 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): -4.297000 34.33100 ymin,ymax (A): -3.440000 48.11900 zmin,zma (A): -23.48600 30.83000 x,y,z range (A): 38.62800 51.55900 54.31600 scale (grids/A): 0.6554238 object centre (A): 15.01700 22.33950 3.672000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 288.3440 centred at (gu) : 90.31649 92.61974 90.00628 assigned negative charge : -285.3443 centred at (gu) : 90.41741 92.75076 89.94025 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5693 nv = 96 ne = 84 npr = 40318 no. pairs analyzed = 40318 no. exposed pairs = 2520 no. arc points = 17340 no. surface atoms = 854 nbur = 1106 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3135 m= 0 mr = 49 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1600000 number of dielectric boundary points 2834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1671 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2747229E-09 1.5668647E-08 midg,1,midg; midg,igrid,midg 1.3845024E-08 -1.7675509E-08 1,midg,midg; igrid,midg,midg 1.8757746E-08 -6.2661352E-09 gauss-seidel spectral radius is 0.9878771 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 14:09:44 rms-change max change #iterations 0.1352182 23.08853 at 10iterations 1.3994396E-02 2.202263 at 20iterations 1.4738154E-03 0.2520180 at 30iterations 1.5096787E-04 2.3468018E-02 at 40iterations 1.5762878E-05 2.4719238E-03 at 50iterations finished qdiffx linear iterations at : 14:09:53 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.5762878E-05 2.4719238E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 14:09:55 3.697u 0.205s 0:15.42 25.2% 0+0k 0+0io 3pf+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 Nov 22 2011 at 14:09:57 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 = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.966271 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): -4.297000 34.33100 ymin,ymax (A): -3.440000 48.11900 zmin,zma (A): -23.48600 30.83000 x,y,z range (A): 38.62800 51.55900 54.31600 scale (grids/A): 1.966271 object centre (A): 15.01700 22.33950 3.672000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 288.3440 centred at (gu) : 90.94946 97.85938 90.01889 assigned negative charge : -285.3443 centred at (gu) : 91.25227 98.25235 89.82101 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17340 grid for indexing accessible points = 1.400000 m= 22727 mr = 42248 m= 3706 mr = 17218 m= 195 mr = 2413 m= 0 mr = 63 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 0.3200000 number of dielectric boundary points 25997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14441 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) : 0.6554238 object centre at (A) : 15.01700 22.33950 3.672000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0086193E-02 1.6092230E-02 midg,1,midg; midg,igrid,midg 4.3238062E-02 -8.6010350E-03 1,midg,midg; igrid,midg,midg 7.0062559E-03 -5.8419481E-03 gauss-seidel spectral radius is 0.9986380 estimated iterations to convergence 215 setup time was (sec) 0.5600000 now iterating at: 14:10:01 rms-change max change #iterations 3.772496 168.4548 at 10iterations 1.777658 67.59795 at 20iterations 0.8325391 32.18402 at 30iterations 0.3890088 13.06693 at 40iterations 0.1828609 6.543861 at 50iterations 8.5656725E-02 2.855682 at 60iterations 4.0039711E-02 1.398228 at 70iterations 1.8732365E-02 0.6746368 at 80iterations 8.7827630E-03 0.3044114 at 90iterations 4.1131601E-03 0.1323251 at 100iterations 1.9268029E-03 6.4147949E-02 at 110iterations 9.0312702E-04 3.0204773E-02 at 120iterations finished qdiffx linear iterations at : 14:10:24 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 9.0312702E-04 3.0204773E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 14:10:25 8.313u 0.236s 0:29.20 29.2% 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 Tue Nov 22 2011 at 14:10:29 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 = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.949407 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): -4.297000 34.33100 ymin,ymax (A): -3.440000 48.11900 zmin,zma (A): -23.48600 30.83000 x,y,z range (A): 38.62800 51.55900 54.31600 scale (grids/A): 2.949407 object centre (A): 15.01700 22.33950 3.672000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 288.3440 centred at (gu) : 91.42419 101.7891 90.02830 assigned negative charge : -285.3443 centred at (gu) : 91.87843 102.3786 89.73160 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 141669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17340 grid for indexing accessible points = 1.400000 m= 72426 mr = 102446 m= 27664 mr = 59885 m= 6862 mr = 22803 m= 915 mr = 5302 m= 33 mr = 597 m= 0 mr = 7 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2192 time to turn everything in is 0.8300000 number of dielectric boundary points 58529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14624 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) : 1.966271 object centre at (A) : 15.01700 22.33950 3.672000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.081756 5.8784444E-02 midg,1,midg; midg,igrid,midg 0.4512238 -0.1632120 1,midg,midg; igrid,midg,midg 3.8849149E-02 -3.8241349E-02 gauss-seidel spectral radius is 0.9992478 estimated iterations to convergence 288 setup time was (sec) 1.090000 now iterating at: 14:10:36 rms-change max change #iterations 8.812557 404.6281 at 10iterations 5.076526 127.9730 at 20iterations 2.919615 60.45581 at 30iterations 1.673776 37.77168 at 40iterations 0.9627206 18.92855 at 50iterations 0.5495943 11.37243 at 60iterations 0.3146618 6.077129 at 70iterations 0.1795822 3.596974 at 80iterations 0.1026277 2.193466 at 90iterations 5.8746621E-02 1.146920 at 100iterations 3.3496540E-02 0.6669025 at 110iterations 1.9181380E-02 0.4074636 at 120iterations 1.0966979E-02 0.2253587 at 130iterations 6.2569310E-03 0.1186773 at 140iterations 3.5671638E-03 6.7785263E-02 at 150iterations 2.0412055E-03 4.6842575E-02 at 160iterations 1.1640402E-03 2.2567749E-02 at 170iterations 6.6517951E-04 1.3702393E-02 at 180iterations finished qdiffx linear iterations at : 14:11:12 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 6.6517951E-04 1.3702393E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 14:11:14 13.481u 0.237s 0:44.90 30.5% 0+0k 0+0io 0pf+0w