Sat Oct 8 16:52:15 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 8 2011 at 16:52:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 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: 0.5607712 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): 15.26600 78.75000 ymin,ymax (A): 127.7080 183.3110 zmin,zma (A): -1.440000 59.80100 x,y,z range (A): 63.48400 55.60299 61.24100 scale (grids/A): 0.5607712 object centre (A): 47.00800 155.5095 29.18050 number of atom coordinates read : 3570 total number of charged atoms : 3452 net assigned charge : -1.499980 assigned positive charge : 542.4696 centred at (gu) : 91.39150 89.30681 88.29450 assigned negative charge : -543.9708 centred at (gu) : 91.36971 89.14576 88.32954 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7445 nv = 96 ne = 84 npr = 70044 no. pairs analyzed = 70044 no. exposed pairs = 4801 no. arc points = 32980 no. surface atoms = 1607 nbur = 1963 mkacc time = 0.1500000 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 = 1.512000 m= 349 mr = 3832 m= 0 mr = 22 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3301 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9627 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0170867E-10 -4.2807355E-10 midg,1,midg; midg,igrid,midg -2.8851364E-09 1.7111530E-09 1,midg,midg; igrid,midg,midg -3.2986033E-10 2.0596305E-10 gauss-seidel spectral radius is 0.9836476 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 16:52:16 rms-change max change #iterations 9.5189452E-02 16.81462 at 10iterations 6.6803019E-03 1.012825 at 20iterations 4.9827324E-04 7.8567505E-02 at 30iterations 6.9735674E-05 9.6216202E-03 at 40iterations 3.0115700E-05 4.3282509E-03 at 50iterations finished qdiffx linear iterations at : 16:52:19 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.0115700E-05 4.3282509E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 16:52:19 3.341u 0.180s 0:03.99 88.2% 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 Sat Oct 8 2011 at 16:52:19 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 = 3570 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.682314 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): 15.26600 78.75000 ymin,ymax (A): 127.7080 183.3110 zmin,zma (A): -1.440000 59.80100 x,y,z range (A): 63.48400 55.60299 61.24100 scale (grids/A): 1.682314 object centre (A): 47.00800 155.5095 29.18050 number of atom coordinates read : 3570 total number of charged atoms : 3452 net assigned charge : -1.499980 assigned positive charge : 542.4696 centred at (gu) : 94.17359 87.91951 84.88262 assigned negative charge : -543.9708 centred at (gu) : 94.10864 87.43684 84.98835 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32980 grid for indexing accessible points = 1.400000 m= 25816 mr = 55092 m= 3142 mr = 17393 m= 125 mr = 1588 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 26618 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) : 0.5607712 object centre at (A) : 47.00800 155.5095 29.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0615105E-03 9.8387757E-03 midg,1,midg; midg,igrid,midg -2.1970056E-02 1.8514412E-02 1,midg,midg; igrid,midg,midg -1.1350693E-02 -2.0608645E-02 gauss-seidel spectral radius is 0.9983681 estimated iterations to convergence 196 setup time was (sec) 0.8800000 now iterating at: 16:52:20 rms-change max change #iterations 3.990411 163.8112 at 10iterations 1.739488 57.27890 at 20iterations 0.7590449 22.98178 at 30iterations 0.3317713 11.72021 at 40iterations 0.1449664 5.258224 at 50iterations 6.3485160E-02 2.014553 at 60iterations 2.7623706E-02 0.9247856 at 70iterations 1.2082426E-02 0.3905153 at 80iterations 5.3007388E-03 0.1795731 at 90iterations 2.3244717E-03 7.7850342E-02 at 100iterations 1.0246526E-03 3.3815265E-02 at 110iterations 4.6423555E-04 1.4416695E-02 at 120iterations finished qdiffx linear iterations at : 16:52:27 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 4.6423555E-04 1.4416695E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 16:52:27 7.555u 0.202s 0:08.07 96.0% 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 Sat Oct 8 2011 at 16:52:27 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 = 3570 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: 2.523470 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): 15.26600 78.75000 ymin,ymax (A): 127.7080 183.3110 zmin,zma (A): -1.440000 59.80100 x,y,z range (A): 63.48400 55.60299 61.24100 scale (grids/A): 2.523470 object centre (A): 47.00800 155.5095 29.18050 number of atom coordinates read : 3570 total number of charged atoms : 3452 net assigned charge : -1.499980 assigned positive charge : 542.4696 centred at (gu) : 96.26006 86.87920 82.32368 assigned negative charge : -543.9708 centred at (gu) : 96.16270 86.15512 82.48241 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 190087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32980 grid for indexing accessible points = 1.400000 m= 87969 mr = 135509 m= 26465 mr = 68365 m= 5087 mr = 19671 m= 512 mr = 3416 m= 14 mr = 285 m= 1 mr = 3 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 82888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 27595 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) : 1.682314 object centre at (A) : 47.00800 155.5095 29.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2227420 0.2685492 midg,1,midg; midg,igrid,midg -0.3143155 0.2976396 1,midg,midg; igrid,midg,midg -0.1936760 -0.3564029 gauss-seidel spectral radius is 0.9992186 estimated iterations to convergence 282 setup time was (sec) 1.690000 now iterating at: 16:52:29 rms-change max change #iterations 10.20242 264.6661 at 10iterations 5.985988 141.7451 at 20iterations 3.484104 84.19360 at 30iterations 2.010849 49.92857 at 40iterations 1.154967 25.91446 at 50iterations 0.6623187 12.53483 at 60iterations 0.3786921 7.619774 at 70iterations 0.2157440 3.836037 at 80iterations 0.1230025 2.285671 at 90iterations 6.9917090E-02 1.423835 at 100iterations 3.9745223E-02 0.7284851 at 110iterations 2.2547603E-02 0.4120426 at 120iterations 1.2825675E-02 0.2445107 at 130iterations 7.2667063E-03 0.1255684 at 140iterations 4.1325060E-03 7.5248122E-02 at 150iterations 2.3504829E-03 4.5000076E-02 at 160iterations 1.3432656E-03 2.9139519E-02 at 170iterations 7.7463652E-04 1.4883041E-02 at 180iterations finished qdiffx linear iterations at : 16:52:41 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 7.7463652E-04 1.4883041E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.69000 DelPhi exited at 16:52:42 13.690u 0.224s 0:14.23 97.7% 0+0k 0+0io 0pf+0w