Sat Oct 15 14:38:07 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 15 2011 at 14:38:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 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: 0.5865972 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): -26.44100 34.24800 ymin,ymax (A): 3.908000 51.68000 zmin,zma (A): -3.453000 55.61900 x,y,z range (A): 60.68900 47.77200 59.07200 scale (grids/A): 0.5865972 object centre (A): 3.903501 27.79400 26.08300 number of atom coordinates read : 3001 total number of charged atoms : 2859 net assigned charge : -2.499965 assigned positive charge : 451.9649 centred at (gu) : 90.22224 90.32385 89.51569 assigned negative charge : -454.4661 centred at (gu) : 90.32501 90.45393 89.43460 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6880 nv = 96 ne = 84 npr = 59518 no. pairs analyzed = 59518 no. exposed pairs = 4068 no. arc points = 28726 no. surface atoms = 1361 nbur = 1640 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 314 mr = 3470 m= 0 mr = 15 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3800000 number of dielectric boundary points 3709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2879 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2883329E-09 1.4213810E-09 midg,1,midg; midg,igrid,midg 2.7144673E-09 -4.6823820E-09 1,midg,midg; igrid,midg,midg 2.0760986E-09 -3.7448853E-09 gauss-seidel spectral radius is 0.9850072 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 14:38:08 rms-change max change #iterations 0.1022741 15.18250 at 10iterations 8.1244987E-03 1.387695 at 20iterations 6.4577529E-04 0.1073756 at 30iterations 5.4216947E-05 9.2182159E-03 at 40iterations 5.1497641E-06 7.8602135E-04 at 50iterations finished qdiffx linear iterations at : 14:38:11 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 5.1497641E-06 7.8602135E-04 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:38:12 4.244u 0.282s 0:04.84 93.3% 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 15 2011 at 14:38:12 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 = 3001 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: 1.759792 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): -26.44100 34.24800 ymin,ymax (A): 3.908000 51.68000 zmin,zma (A): -3.453000 55.61900 x,y,z range (A): 60.68900 47.77200 59.07200 scale (grids/A): 1.759792 object centre (A): 3.903501 27.79400 26.08300 number of atom coordinates read : 3001 total number of charged atoms : 2859 net assigned charge : -2.499965 assigned positive charge : 451.9649 centred at (gu) : 90.66628 90.97070 88.54604 assigned negative charge : -454.4661 centred at (gu) : 90.97480 91.36120 88.30337 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28726 grid for indexing accessible points = 1.400000 m= 23831 mr = 50096 m= 2773 mr = 16332 m= 112 mr = 1414 m= 0 mr = 16 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 930 time to turn everything in is 0.6600000 number of dielectric boundary points 34167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 22237 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) : 0.5865972 object centre at (A) : 3.903501 27.79400 26.08300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4354345E-03 1.8733012E-02 midg,1,midg; midg,igrid,midg 6.3644801E-03 -1.9238852E-02 1,midg,midg; igrid,midg,midg 2.2209920E-02 -2.9879337E-02 gauss-seidel spectral radius is 0.9984574 estimated iterations to convergence 202 setup time was (sec) 0.9500000 now iterating at: 14:38:13 rms-change max change #iterations 3.942055 169.6612 at 10iterations 1.741950 70.30064 at 20iterations 0.7763694 24.30318 at 30iterations 0.3465276 10.84880 at 40iterations 0.1543454 5.015831 at 50iterations 6.8951890E-02 2.269281 at 60iterations 3.0645316E-02 0.9783516 at 70iterations 1.3731947E-02 0.4471664 at 80iterations 6.1154850E-03 0.2082148 at 90iterations 2.7326080E-03 8.7169647E-02 at 100iterations 1.2155009E-03 4.2755127E-02 at 110iterations 5.4323999E-04 1.7178059E-02 at 120iterations finished qdiffx linear iterations at : 14:38:22 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 5.4323999E-04 1.7178059E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 14:38:22 9.808u 0.369s 0:10.66 95.3% 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 15 2011 at 14:38:22 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 = 3001 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: 2.639688 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): -26.44100 34.24800 ymin,ymax (A): 3.908000 51.68000 zmin,zma (A): -3.453000 55.61900 x,y,z range (A): 60.68900 47.77200 59.07200 scale (grids/A): 2.639688 object centre (A): 3.903501 27.79400 26.08300 number of atom coordinates read : 3001 total number of charged atoms : 2859 net assigned charge : -2.499965 assigned positive charge : 451.9649 centred at (gu) : 90.99910 91.45595 87.81879 assigned negative charge : -454.4661 centred at (gu) : 91.46210 92.04159 87.45493 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 174549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28726 grid for indexing accessible points = 1.400000 m= 80582 mr = 122622 m= 24837 mr = 63380 m= 4456 mr = 18542 m= 386 mr = 2940 m= 12 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 3334 time to turn everything in is 1.670000 number of dielectric boundary points 77149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 22868 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) : 1.759792 object centre at (A) : 3.903501 27.79400 26.08300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1746190 0.2758767 midg,1,midg; midg,igrid,midg 7.5878747E-02 -0.2141088 1,midg,midg; igrid,midg,midg 0.3815913 -0.3435601 gauss-seidel spectral radius is 0.9992298 estimated iterations to convergence 284 setup time was (sec) 2.010000 now iterating at: 14:38:25 rms-change max change #iterations 9.819415 307.0767 at 10iterations 5.732696 150.7935 at 20iterations 3.294904 75.38596 at 30iterations 1.893600 43.66424 at 40iterations 1.089059 23.53103 at 50iterations 0.6214783 13.56089 at 60iterations 0.3548690 7.296303 at 70iterations 0.2020037 4.174573 at 80iterations 0.1154291 2.243108 at 90iterations 6.5565750E-02 1.262646 at 100iterations 3.7323676E-02 0.6939831 at 110iterations 2.1140546E-02 0.4071579 at 120iterations 1.2002781E-02 0.2167397 at 130iterations 6.8258080E-03 0.1226196 at 140iterations 3.8768922E-03 7.5873375E-02 at 150iterations 2.2027378E-03 4.1297913E-02 at 160iterations 1.2507903E-03 2.4455070E-02 at 170iterations 7.0929108E-04 1.4222622E-02 at 180iterations finished qdiffx linear iterations at : 14:38:39 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 7.0929108E-04 1.4222622E-02 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.64000 DelPhi exited at 14:38:40 16.637u 0.356s 0:17.43 97.4% 0+0k 0+0io 0pf+0w