Mon Oct 10 10:23:51 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 Mon Oct 10 2011 at 10:23:51 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 = 2797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5911755 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): -18.18600 33.43400 ymin,ymax (A): -59.68600 -0.7170001 zmin,zma (A): -1.360000 58.85900 x,y,z range (A): 51.62000 58.96900 60.21900 scale (grids/A): 0.5911755 object centre (A): 7.624000 -30.20150 28.74950 number of atom coordinates read : 2797 total number of charged atoms : 2647 net assigned charge : 5.000009 assigned positive charge : 408.3260 centred at (gu) : 88.53213 88.37784 88.06944 assigned negative charge : -403.3264 centred at (gu) : 88.62752 88.23985 87.98268 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6600 nv = 96 ne = 84 npr = 54813 no. pairs analyzed = 54813 no. exposed pairs = 4302 no. arc points = 31098 no. surface atoms = 1420 nbur = 1377 mkacc time = 0.1200000 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= 344 mr = 2801 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3033 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8185 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3555466E-09 2.6522646E-09 midg,1,midg; midg,igrid,midg -3.4458540E-09 3.8165173E-09 1,midg,midg; igrid,midg,midg 6.1165406E-09 -7.4197831E-10 gauss-seidel spectral radius is 0.9852332 estimated iterations to convergence 68 setup time was (sec) 0.5100000 now iterating at: 10:23:51 rms-change max change #iterations 9.9162705E-02 15.96133 at 10iterations 8.1476681E-03 1.331688 at 20iterations 6.5854972E-04 0.1007376 at 30iterations 5.9535698E-05 9.1400146E-03 at 40iterations 8.0072286E-06 1.0681152E-03 at 50iterations finished qdiffx linear iterations at : 10:23:54 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 8.0072286E-06 1.0681152E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 10:23:54 3.076u 0.149s 0:03.52 91.1% 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 Mon Oct 10 2011 at 10:23:54 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 = 2797 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: 1.773527 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): -18.18600 33.43400 ymin,ymax (A): -59.68600 -0.7170001 zmin,zma (A): -1.360000 58.85900 x,y,z range (A): 51.62000 58.96900 60.21900 scale (grids/A): 1.773527 object centre (A): 7.624000 -30.20150 28.74950 number of atom coordinates read : 2797 total number of charged atoms : 2647 net assigned charge : 5.000009 assigned positive charge : 408.3260 centred at (gu) : 85.59595 85.13292 84.20802 assigned negative charge : -403.3264 centred at (gu) : 85.88258 84.71953 83.94777 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31098 grid for indexing accessible points = 1.400000 m= 22148 mr = 41724 m= 3015 mr = 13926 m= 130 mr = 1338 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 38166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 243 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20646 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) : 0.5911755 object centre at (A) : 7.624000 -30.20150 28.74950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1768931E-02 9.6920757E-03 midg,1,midg; midg,igrid,midg 1.6924398E-02 3.3473250E-02 1,midg,midg; igrid,midg,midg 1.0234089E-02 1.8632531E-03 gauss-seidel spectral radius is 0.9984754 estimated iterations to convergence 203 setup time was (sec) 0.7500000 now iterating at: 10:23:55 rms-change max change #iterations 3.762588 161.0983 at 10iterations 1.676172 64.82919 at 20iterations 0.7472883 25.02359 at 30iterations 0.3328758 11.26154 at 40iterations 0.1491499 4.794043 at 50iterations 6.6637821E-02 2.344400 at 60iterations 2.9830778E-02 1.051174 at 70iterations 1.3316932E-02 0.4773750 at 80iterations 5.9601562E-03 0.2002645 at 90iterations 2.6583923E-03 0.1022196 at 100iterations 1.1929781E-03 4.1711330E-02 at 110iterations 5.3547678E-04 2.0888329E-02 at 120iterations finished qdiffx linear iterations at : 10:24:01 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 5.3547678E-04 2.0888329E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 10:24:02 6.932u 0.177s 0:07.44 95.4% 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 10:24:02 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 = 2797 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: 2.660290 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): -18.18600 33.43400 ymin,ymax (A): -59.68600 -0.7170001 zmin,zma (A): -1.360000 58.85900 x,y,z range (A): 51.62000 58.96900 60.21900 scale (grids/A): 2.660290 object centre (A): 7.624000 -30.20150 28.74950 number of atom coordinates read : 2797 total number of charged atoms : 2647 net assigned charge : 5.000009 assigned positive charge : 408.3260 centred at (gu) : 83.39373 82.69931 81.31197 assigned negative charge : -403.3264 centred at (gu) : 83.82382 82.07917 80.92152 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 161075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31098 grid for indexing accessible points = 1.400000 m= 71747 mr = 103265 m= 23966 mr = 52590 m= 4969 mr = 17143 m= 506 mr = 3047 m= 16 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 86023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 21170 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) : 1.773527 object centre at (A) : 7.624000 -30.20150 28.74950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3407716 7.1671747E-02 midg,1,midg; midg,igrid,midg 0.3694333 0.4226883 1,midg,midg; igrid,midg,midg 4.9614094E-02 5.0877184E-02 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.500000 now iterating at: 10:24:04 rms-change max change #iterations 9.570467 294.6586 at 10iterations 5.739223 142.4038 at 20iterations 3.387734 80.84195 at 30iterations 1.985793 54.55930 at 40iterations 1.156124 28.23055 at 50iterations 0.6702735 15.79622 at 60iterations 0.3880135 8.362404 at 70iterations 0.2236275 4.907982 at 80iterations 0.1288757 3.165097 at 90iterations 7.4077494E-02 1.771570 at 100iterations 4.2557072E-02 0.9981728 at 110iterations 2.4364283E-02 0.4954486 at 120iterations 1.3985238E-02 0.2929630 at 130iterations 8.0244178E-03 0.1650028 at 140iterations 4.5920466E-03 8.8273287E-02 at 150iterations 2.6288957E-03 5.7855606E-02 at 160iterations 1.5045797E-03 3.3500671E-02 at 170iterations 8.6172670E-04 1.8102169E-02 at 180iterations finished qdiffx linear iterations at : 10:24:13 total time elapsed so far: 10.99000 # loops : 180 mean,max change (kT/e) : 8.6172670E-04 1.8102169E-02 energy calculations done at 10.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 10:24:14 11.178u 0.176s 0:11.62 97.5% 0+0k 0+0io 0pf+0w