Sun Oct 9 23:48:11 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 23:48:11 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 0.6028381 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): -28.41000 30.64400 ymin,ymax (A): 8.096001 62.14400 zmin,zma (A): 24.92500 77.29500 x,y,z range (A): 59.05400 54.04800 52.37000 scale (grids/A): 0.6028381 object centre (A): 1.117000 35.12000 51.11000 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -0.9749913 assigned positive charge : 471.7190 centred at (gu) : 89.44485 89.01051 88.98550 assigned negative charge : -472.6952 centred at (gu) : 89.49203 89.00970 89.10200 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7600 nv = 96 ne = 84 npr = 62540 no. pairs analyzed = 62540 no. exposed pairs = 4066 no. arc points = 28824 no. surface atoms = 1360 nbur = 1773 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 4009 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3200000 number of dielectric boundary points 3945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2897 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3755290E-09 -4.9576916E-09 midg,1,midg; midg,igrid,midg -7.1083506E-10 -3.9665543E-10 1,midg,midg; igrid,midg,midg 1.9826545E-09 -2.4925633E-09 gauss-seidel spectral radius is 0.9858078 estimated iterations to convergence 69 setup time was (sec) 0.5300000 now iterating at: 23:48:12 rms-change max change #iterations 0.1213331 16.35922 at 10iterations 1.0587562E-02 1.468563 at 20iterations 9.1366400E-04 0.1388054 at 30iterations 7.9540507E-05 1.2351036E-02 at 40iterations 7.7140548E-06 1.1249781E-03 at 50iterations finished qdiffx linear iterations at : 23:48:14 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 7.7140548E-06 1.1249781E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 23:48:15 3.119u 0.136s 0:03.54 91.5% 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 23:48:15 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.808514 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): -28.41000 30.64400 ymin,ymax (A): 8.096001 62.14400 zmin,zma (A): 24.92500 77.29500 x,y,z range (A): 59.05400 54.04800 52.37000 scale (grids/A): 1.808514 object centre (A): 1.117000 35.12000 51.11000 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -0.9749913 assigned positive charge : 471.7190 centred at (gu) : 88.33381 87.03110 86.95588 assigned negative charge : -472.6952 centred at (gu) : 88.47580 87.02895 87.30556 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28824 grid for indexing accessible points = 1.400000 m= 27212 mr = 56685 m= 3610 mr = 19160 m= 137 mr = 1998 m= 0 mr = 28 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 396 time to turn everything in is 0.5600000 number of dielectric boundary points 36352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 23296 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) : 0.6028381 object centre at (A) : 1.117000 35.12000 51.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4648803E-03 -4.8992322E-03 midg,1,midg; midg,igrid,midg 6.4885421E-03 6.9603818E-03 1,midg,midg; igrid,midg,midg 7.4020084E-03 -1.1475806E-02 gauss-seidel spectral radius is 0.9985561 estimated iterations to convergence 209 setup time was (sec) 0.8200000 now iterating at: 23:48:16 rms-change max change #iterations 4.277129 174.1756 at 10iterations 1.943767 66.34154 at 20iterations 0.8918496 29.30359 at 30iterations 0.4066626 12.57575 at 40iterations 0.1869114 5.648005 at 50iterations 8.5098967E-02 2.815618 at 60iterations 3.9075743E-02 1.236328 at 70iterations 1.7930597E-02 0.5579352 at 80iterations 8.2257474E-03 0.2597961 at 90iterations 3.7523743E-03 0.1157017 at 100iterations 1.7203517E-03 5.6694984E-02 at 110iterations 7.9049781E-04 2.4605751E-02 at 120iterations finished qdiffx linear iterations at : 23:48:22 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 7.9049781E-04 2.4605751E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 23:48:22 6.996u 0.152s 0:07.52 94.9% 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 Sun Oct 9 2011 at 23:48:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.712771 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): -28.41000 30.64400 ymin,ymax (A): 8.096001 62.14400 zmin,zma (A): 24.92500 77.29500 x,y,z range (A): 59.05400 54.04800 52.37000 scale (grids/A): 2.712771 object centre (A): 1.117000 35.12000 51.11000 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -0.9749913 assigned positive charge : 471.7190 centred at (gu) : 87.50027 85.54634 85.43364 assigned negative charge : -472.6952 centred at (gu) : 87.71368 85.54316 85.95818 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 192997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28824 grid for indexing accessible points = 1.400000 m= 91322 mr = 138095 m= 29033 mr = 72921 m= 5853 mr = 22300 m= 665 mr = 4207 m= 23 mr = 378 m= 0 mr = 3 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 1293 time to turn everything in is 1.380000 number of dielectric boundary points 81989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 23887 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) : 1.808514 object centre at (A) : 1.117000 35.12000 51.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1239914 1.0117677E-02 midg,1,midg; midg,igrid,midg 2.9259894E-02 0.1150747 1,midg,midg; igrid,midg,midg -8.4257312E-03 -0.1443251 gauss-seidel spectral radius is 0.9992601 estimated iterations to convergence 290 setup time was (sec) 1.660000 now iterating at: 23:48:24 rms-change max change #iterations 10.49042 286.1820 at 10iterations 6.240412 146.6613 at 20iterations 3.671270 75.04831 at 30iterations 2.145762 44.70178 at 40iterations 1.255650 23.23981 at 50iterations 0.7291094 14.74541 at 60iterations 0.4233415 7.835197 at 70iterations 0.2449798 5.165336 at 80iterations 0.1416569 2.610580 at 90iterations 8.2009993E-02 1.476331 at 100iterations 4.7302004E-02 0.8587027 at 110iterations 2.7248539E-02 0.5905571 at 120iterations 1.5735710E-02 0.2962766 at 130iterations 9.0392753E-03 0.1612997 at 140iterations 5.2090460E-03 9.5088959E-02 at 150iterations 3.0006422E-03 5.2124798E-02 at 160iterations 1.7279532E-03 2.9726028E-02 at 170iterations 9.9412142E-04 1.6693115E-02 at 180iterations finished qdiffx linear iterations at : 23:48:33 total time elapsed so far: 11.12000 # loops : 180 mean,max change (kT/e) : 9.9412142E-04 1.6693115E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 23:48:34 11.292u 0.172s 0:11.80 97.1% 0+0k 0+0io 0pf+0w