Tue Oct 11 06:20:29 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 Tue Oct 11 2011 at 06:20:29 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 = 2034 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: 0.6849710 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): 17.22400 63.72700 ymin,ymax (A): -3.557000 34.05600 zmin,zma (A): 18.83700 70.81000 x,y,z range (A): 46.50300 37.61300 51.97300 scale (grids/A): 0.6849710 object centre (A): 40.47550 15.24950 44.82350 number of atom coordinates read : 2034 total number of charged atoms : 1952 net assigned charge : 6.500006 assigned positive charge : 315.0320 centred at (gu) : 90.70522 89.42121 89.88335 assigned negative charge : -308.5322 centred at (gu) : 90.84876 89.48463 89.88955 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6531 nv = 96 ne = 84 npr = 39334 no. pairs analyzed = 39334 no. exposed pairs = 2545 no. arc points = 17757 no. surface atoms = 862 nbur = 1172 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3609 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1811 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4511878E-08 2.9458455E-08 midg,1,midg; midg,igrid,midg 5.6416297E-08 1.2043930E-08 1,midg,midg; igrid,midg,midg 6.3535069E-08 -1.2455471E-08 gauss-seidel spectral radius is 0.9888952 estimated iterations to convergence 77 setup time was (sec) 0.3500000 now iterating at: 06:20:30 rms-change max change #iterations 0.1710417 27.50777 at 10iterations 1.9474845E-02 2.866451 at 20iterations 2.2518595E-03 0.2921162 at 30iterations 2.9259408E-04 4.2423248E-02 at 40iterations 4.8019756E-05 8.3146095E-03 at 50iterations finished qdiffx linear iterations at : 06:20:33 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.8019756E-05 8.3146095E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:20:33 3.326u 0.171s 0:03.84 90.8% 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 Tue Oct 11 2011 at 06:20:33 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 = 2034 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: 2.054913 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): 17.22400 63.72700 ymin,ymax (A): -3.557000 34.05600 zmin,zma (A): 18.83700 70.81000 x,y,z range (A): 46.50300 37.61300 51.97300 scale (grids/A): 2.054913 object centre (A): 40.47550 15.24950 44.82350 number of atom coordinates read : 2034 total number of charged atoms : 1952 net assigned charge : 6.500006 assigned positive charge : 315.0320 centred at (gu) : 92.11561 88.26371 89.65039 assigned negative charge : -308.5322 centred at (gu) : 92.54653 88.45390 89.66875 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69647 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17757 grid for indexing accessible points = 1.400000 m= 27191 mr = 48646 m= 4928 mr = 20250 m= 415 mr = 3214 m= 13 mr = 197 m= 0 mr = 5 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15481 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) : 0.6849710 object centre at (A) : 40.47550 15.24950 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4361498E-02 4.4519294E-02 midg,1,midg; midg,igrid,midg 2.8412335E-02 -4.3322314E-03 1,midg,midg; igrid,midg,midg 2.9764030E-02 1.4622894E-02 gauss-seidel spectral radius is 0.9987626 estimated iterations to convergence 225 setup time was (sec) 0.5700000 now iterating at: 06:20:34 rms-change max change #iterations 4.307129 269.8257 at 10iterations 2.097020 84.95374 at 20iterations 1.014800 32.48779 at 30iterations 0.4951129 15.24790 at 40iterations 0.2404832 7.511373 at 50iterations 0.1169474 3.914980 at 60iterations 5.6899820E-02 1.727747 at 70iterations 2.7681362E-02 0.8732014 at 80iterations 1.3461507E-02 0.4238772 at 90iterations 6.5324348E-03 0.1990395 at 100iterations 3.1995443E-03 0.1107521 at 110iterations 1.5604930E-03 5.0857544E-02 at 120iterations finished qdiffx linear iterations at : 06:20:41 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.5604930E-03 5.0857544E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 06:20:42 7.879u 0.197s 0:08.57 94.0% 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 Oct 11 2011 at 06:20:42 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 = 2034 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: 3.082370 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): 17.22400 63.72700 ymin,ymax (A): -3.557000 34.05600 zmin,zma (A): 18.83700 70.81000 x,y,z range (A): 46.50300 37.61300 51.97300 scale (grids/A): 3.082370 object centre (A): 40.47550 15.24950 44.82350 number of atom coordinates read : 2034 total number of charged atoms : 1952 net assigned charge : 6.500006 assigned positive charge : 315.0320 centred at (gu) : 93.17337 87.39548 89.47546 assigned negative charge : -308.5322 centred at (gu) : 93.81976 87.68090 89.50314 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 160508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17757 grid for indexing accessible points = 1.400000 m= 85418 mr = 117352 m= 33780 mr = 70400 m= 9304 mr = 27334 m= 1717 mr = 7113 m= 179 mr = 1224 m= 4 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 67392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 15616 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) : 2.054913 object centre at (A) : 40.47550 15.24950 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3705526 0.2821995 midg,1,midg; midg,igrid,midg 0.2449385 -3.3816144E-02 1,midg,midg; igrid,midg,midg 0.2198374 0.2598144 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.290000 now iterating at: 06:20:43 rms-change max change #iterations 9.804731 350.8441 at 10iterations 5.783158 122.6942 at 20iterations 3.407613 71.08795 at 30iterations 1.999704 37.51459 at 40iterations 1.169585 23.31926 at 50iterations 0.6847348 12.70662 at 60iterations 0.4000301 7.600849 at 70iterations 0.2328102 4.215307 at 80iterations 0.1362184 2.561386 at 90iterations 7.9359993E-02 1.816605 at 100iterations 4.6190150E-02 0.8141947 at 110iterations 2.6944313E-02 0.5263809 at 120iterations 1.5699973E-02 0.2726250 at 130iterations 9.1798455E-03 0.1684914 at 140iterations 5.3888061E-03 0.1019306 at 150iterations 3.2038344E-03 6.7253113E-02 at 160iterations 1.9285395E-03 4.0442467E-02 at 170iterations 1.1991343E-03 2.6062012E-02 at 180iterations finished qdiffx linear iterations at : 06:20:55 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 1.1991343E-03 2.6062012E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 06:20:55 12.668u 0.213s 0:13.16 97.7% 0+0k 0+0io 0pf+0w