Mon Oct 10 09:44:30 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 Mon Oct 10 2011 at 09:44:30 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5796441 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): -17.64700 34.03300 ymin,ymax (A): -59.83700 -0.9110001 zmin,zma (A): -0.5100000 60.90700 x,y,z range (A): 51.68000 58.92600 61.41700 scale (grids/A): 0.5796441 object centre (A): 8.192999 -30.37400 30.19850 number of atom coordinates read : 2737 total number of charged atoms : 2590 net assigned charge : 8.014017 assigned positive charge : 401.6781 centred at (gu) : 87.97958 88.01465 87.99783 assigned negative charge : -393.6645 centred at (gu) : 88.00143 87.88440 87.92804 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6319 nv = 96 ne = 84 npr = 51912 no. pairs analyzed = 51912 no. exposed pairs = 4176 no. arc points = 30741 no. surface atoms = 1387 nbur = 1350 mkacc time = 9.0000004E-02 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 = 1.484000 m= 330 mr = 2720 m= 4 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7838 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6012867E-10 1.9559856E-09 midg,1,midg; midg,igrid,midg -1.2388330E-09 2.6650466E-09 1,midg,midg; igrid,midg,midg 3.5093157E-09 8.7429547E-10 gauss-seidel spectral radius is 0.9846421 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 09:44:30 rms-change max change #iterations 9.3759894E-02 14.77945 at 10iterations 7.2120358E-03 1.129150 at 20iterations 5.7427894E-04 9.6250534E-02 at 30iterations 5.3538282E-05 8.1396103E-03 at 40iterations 7.9860411E-06 1.0375977E-03 at 50iterations finished qdiffx linear iterations at : 09:44:33 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.9860411E-06 1.0375977E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 09:44:34 3.359u 0.158s 0:03.81 91.8% 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 Mon Oct 10 2011 at 09:44:34 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.738932 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): -17.64700 34.03300 ymin,ymax (A): -59.83700 -0.9110001 zmin,zma (A): -0.5100000 60.90700 x,y,z range (A): 51.68000 58.92600 61.41700 scale (grids/A): 1.738932 object centre (A): 8.192999 -30.37400 30.19850 number of atom coordinates read : 2737 total number of charged atoms : 2590 net assigned charge : 8.014017 assigned positive charge : 401.6781 centred at (gu) : 83.93823 84.04353 83.99295 assigned negative charge : -393.6645 centred at (gu) : 84.00418 83.65309 83.78397 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30741 grid for indexing accessible points = 1.400000 m= 20945 mr = 40406 m= 2864 mr = 13138 m= 139 mr = 1286 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 36457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20116 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) : 0.5796441 object centre at (A) : 8.192999 -30.37400 30.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0014199E-03 2.0364111E-03 midg,1,midg; midg,igrid,midg 3.0286733E-02 2.6913460E-02 1,midg,midg; igrid,midg,midg 1.1515090E-02 4.2467574E-03 gauss-seidel spectral radius is 0.9984092 estimated iterations to convergence 199 setup time was (sec) 0.5500000 now iterating at: 09:44:34 rms-change max change #iterations 3.623759 170.7703 at 10iterations 1.590755 64.52336 at 20iterations 0.7018181 30.11972 at 30iterations 0.3079827 12.38488 at 40iterations 0.1358709 4.995538 at 50iterations 5.9687451E-02 2.173237 at 60iterations 2.6289219E-02 1.026294 at 70iterations 1.1563649E-02 0.4062004 at 80iterations 5.0760265E-03 0.1814728 at 90iterations 2.2414671E-03 8.4955215E-02 at 100iterations 9.8797306E-04 3.5681725E-02 at 110iterations 4.3444813E-04 1.5792370E-02 at 120iterations finished qdiffx linear iterations at : 09:44:42 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 4.3444813E-04 1.5792370E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 09:44:43 7.786u 0.217s 0:08.89 89.8% 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 Mon Oct 10 2011 at 09:44:43 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.608398 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): -17.64700 34.03300 ymin,ymax (A): -59.83700 -0.9110001 zmin,zma (A): -0.5100000 60.90700 x,y,z range (A): 51.68000 58.92600 61.41700 scale (grids/A): 2.608398 object centre (A): 8.192999 -30.37400 30.19850 number of atom coordinates read : 2737 total number of charged atoms : 2590 net assigned charge : 8.014017 assigned positive charge : 401.6781 centred at (gu) : 80.90720 81.06510 80.98933 assigned negative charge : -393.6645 centred at (gu) : 81.00616 80.47951 80.67581 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30741 grid for indexing accessible points = 1.400000 m= 68555 mr = 100144 m= 22254 mr = 50658 m= 4628 mr = 15651 m= 473 mr = 2795 m= 21 mr = 204 m= 0 mr = 1 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 82227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20712 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) : 1.738932 object centre at (A) : 8.192999 -30.37400 30.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1946247 -3.8671412E-02 midg,1,midg; midg,igrid,midg 0.5939617 0.3662440 1,midg,midg; igrid,midg,midg 5.3985927E-02 5.0862994E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.100000 now iterating at: 09:44:44 rms-change max change #iterations 9.387401 299.8970 at 10iterations 5.573369 166.9129 at 20iterations 3.268315 82.13221 at 30iterations 1.896775 49.06178 at 40iterations 1.096293 31.86524 at 50iterations 0.6323652 17.55331 at 60iterations 0.3627265 9.172817 at 70iterations 0.2079556 4.783943 at 80iterations 0.1186615 2.683508 at 90iterations 6.7560576E-02 1.520809 at 100iterations 3.8434658E-02 0.9241406 at 110iterations 2.1926368E-02 0.4633789 at 120iterations 1.2450849E-02 0.2667618 at 130iterations 7.0737796E-03 0.1409836 at 140iterations 4.0149121E-03 9.0530396E-02 at 150iterations 2.2806460E-03 4.5373082E-02 at 160iterations 1.2932315E-03 2.6087761E-02 at 170iterations 7.3326618E-04 1.5116215E-02 at 180iterations finished qdiffx linear iterations at : 09:44:56 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 7.3326618E-04 1.5116215E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 09:44:56 12.853u 0.247s 0:13.45 97.3% 0+0k 0+0io 0pf+0w