Sat Oct 8 18:17:13 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 Sat Oct 8 2011 at 18:17:13 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3752 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: 0.5431300 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): -1.687000 60.34600 ymin,ymax (A): -18.58500 44.38600 zmin,zma (A): -6.439000 59.10700 x,y,z range (A): 62.03300 62.97100 65.54601 scale (grids/A): 0.5431300 object centre (A): 29.32950 12.90050 26.33400 number of atom coordinates read : 3752 total number of charged atoms : 3601 net assigned charge : -9.999962 assigned positive charge : 571.8843 centred at (gu) : 88.80856 86.81599 90.72020 assigned negative charge : -581.8868 centred at (gu) : 88.88883 86.83582 90.74794 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7205 nv = 96 ne = 84 npr = 75523 no. pairs analyzed = 75523 no. exposed pairs = 4880 no. arc points = 34579 no. surface atoms = 1625 nbur = 2127 mkacc time = 0.2200000 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 = 1.596000 m= 308 mr = 3676 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3467 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9345751E-10 -9.2377295E-10 midg,1,midg; midg,igrid,midg -8.7965163E-10 -3.3260467E-10 1,midg,midg; igrid,midg,midg 8.0080137E-11 -8.8325264E-10 gauss-seidel spectral radius is 0.9825856 estimated iterations to convergence 62 setup time was (sec) 0.7300000 now iterating at: 18:17:14 rms-change max change #iterations 8.2271188E-02 14.05781 at 10iterations 5.6096953E-03 0.8986292 at 20iterations 5.2241061E-04 8.2576752E-02 at 30iterations 1.1354843E-04 1.7985821E-02 at 40iterations 3.3408091E-05 5.1870346E-03 at 50iterations finished qdiffx linear iterations at : 18:17:17 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 3.3408091E-05 5.1870346E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 18:17:18 4.247u 0.283s 0:04.80 94.1% 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 18:17:18 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3752 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: 1.629390 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): -1.687000 60.34600 ymin,ymax (A): -18.58500 44.38600 zmin,zma (A): -6.439000 59.10700 x,y,z range (A): 62.03300 62.97100 65.54601 scale (grids/A): 1.629390 object centre (A): 29.32950 12.90050 26.33400 number of atom coordinates read : 3752 total number of charged atoms : 3601 net assigned charge : -9.999962 assigned positive charge : 571.8843 centred at (gu) : 86.42452 80.44685 92.15923 assigned negative charge : -581.8868 centred at (gu) : 86.66601 80.50723 92.24358 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 79510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34579 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24602 mr = 53516 m= 2491 mr = 16491 m= 60 mr = 1085 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.7300000 number of dielectric boundary points 35571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 27537 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) : 0.5431300 object centre at (A) : 29.32950 12.90050 26.33400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1444166E-04 -1.1267267E-02 midg,1,midg; midg,igrid,midg -2.5994891E-02 -7.2292807E-03 1,midg,midg; igrid,midg,midg -1.0142559E-02 -2.9340670E-02 gauss-seidel spectral radius is 0.9982505 estimated iterations to convergence 190 setup time was (sec) 1.030000 now iterating at: 18:17:19 rms-change max change #iterations 3.846680 183.8584 at 10iterations 1.625256 56.97752 at 20iterations 0.6867594 25.63375 at 30iterations 0.2902099 10.41510 at 40iterations 0.1232056 4.171616 at 50iterations 5.2228540E-02 2.026299 at 60iterations 2.2237413E-02 0.7343409 at 70iterations 9.4273910E-03 0.2978516 at 80iterations 4.0097279E-03 0.1203785 at 90iterations 1.7145658E-03 6.1340332E-02 at 100iterations 7.4217486E-04 2.8347015E-02 at 110iterations 3.2602978E-04 1.1415839E-02 at 120iterations finished qdiffx linear iterations at : 18:17:27 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 3.2602978E-04 1.1415839E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 18:17:28 9.708u 0.296s 0:10.27 97.2% 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 18:17:28 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3752 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: 2.444085 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): -1.687000 60.34600 ymin,ymax (A): -18.58500 44.38600 zmin,zma (A): -6.439000 59.10700 x,y,z range (A): 62.03300 62.97100 65.54601 scale (grids/A): 2.444085 object centre (A): 29.32950 12.90050 26.33400 number of atom coordinates read : 3752 total number of charged atoms : 3601 net assigned charge : -9.999962 assigned positive charge : 571.8843 centred at (gu) : 84.63641 75.67013 93.23859 assigned negative charge : -581.8868 centred at (gu) : 84.99895 75.76069 93.36541 start vw surface at 0.2000000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 184827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34579 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85114 mr = 131382 m= 23993 mr = 66425 m= 3881 mr = 17590 m= 216 mr = 2312 m= 7 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 1.790000 number of dielectric boundary points 80266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 28758 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) : 1.629390 object centre at (A) : 29.32950 12.90050 26.33400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6147880E-02 3.7631132E-02 midg,1,midg; midg,igrid,midg -0.3974282 -9.7511567E-02 1,midg,midg; igrid,midg,midg -0.1706535 -0.5474940 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 2.120000 now iterating at: 18:17:30 rms-change max change #iterations 10.00123 271.5714 at 10iterations 5.686360 126.1501 at 20iterations 3.224865 67.99191 at 30iterations 1.815492 38.49759 at 40iterations 1.020941 21.81216 at 50iterations 0.5719073 10.60483 at 60iterations 0.3202751 7.053578 at 70iterations 0.1794772 3.439197 at 80iterations 0.1001415 1.854368 at 90iterations 5.5811208E-02 0.9998980 at 100iterations 3.1165479E-02 0.5831299 at 110iterations 1.7380174E-02 0.3151618 at 120iterations 9.6917497E-03 0.2002778 at 130iterations 5.4142503E-03 0.1014746 at 140iterations 3.0272428E-03 6.0010910E-02 at 150iterations 1.6970688E-03 2.9755592E-02 at 160iterations 9.5116068E-04 1.9644737E-02 at 170iterations 5.4008781E-04 1.0768652E-02 at 180iterations finished qdiffx linear iterations at : 18:17:44 total time elapsed so far: 16.31000 # loops : 180 mean,max change (kT/e) : 5.4008781E-04 1.0768652E-02 energy calculations done at 16.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 18:17:45 16.499u 0.297s 0:17.08 98.2% 0+0k 0+0io 0pf+0w