Sat Oct 8 18:30:26 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 18:30:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6246052 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): -31.49400 17.34300 ymin,ymax (A): -23.58000 22.88600 zmin,zma (A): -12.49200 44.50400 x,y,z range (A): 48.83700 46.46600 56.99600 scale (grids/A): 0.6246052 object centre (A): -7.075500 -0.3470001 16.00600 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.40051 89.24429 89.89659 assigned negative charge : -387.4045 centred at (gu) : 88.30022 89.28607 89.78144 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6558 nv = 96 ne = 84 npr = 54878 no. pairs analyzed = 54878 no. exposed pairs = 2901 no. arc points = 20747 no. surface atoms = 989 nbur = 1605 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3741 m= 0 mr = 44 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.2000000 number of dielectric boundary points 3094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1071960E-09 1.2126049E-08 midg,1,midg; midg,igrid,midg 8.2061815E-09 5.7894806E-10 1,midg,midg; igrid,midg,midg -5.6058838E-09 7.9925462E-09 gauss-seidel spectral radius is 0.9867168 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 18:30:26 rms-change max change #iterations 0.1337881 20.20071 at 10iterations 1.2384526E-02 2.002817 at 20iterations 1.1761350E-03 0.1650810 at 30iterations 1.0937461E-04 1.4918327E-02 at 40iterations 1.0412090E-05 1.5754700E-03 at 50iterations finished qdiffx linear iterations at : 18:30:29 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.0412090E-05 1.5754700E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 18:30:30 3.644u 0.193s 0:04.10 93.4% 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 Sat Oct 8 2011 at 18:30:30 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.873816 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): -31.49400 17.34300 ymin,ymax (A): -23.58000 22.88600 zmin,zma (A): -12.49200 44.50400 x,y,z range (A): 48.83700 46.46600 56.99600 scale (grids/A): 1.873816 object centre (A): -7.075500 -0.3470001 16.00600 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.20085 87.73232 89.68922 assigned negative charge : -387.4045 centred at (gu) : 84.90014 87.85797 89.34404 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20747 grid for indexing accessible points = 1.400000 m= 24722 mr = 50457 m= 3497 mr = 18547 m= 176 mr = 2246 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9440 time to turn everything in is 0.3500000 number of dielectric boundary points 28481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19248 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) : 0.6246052 object centre at (A) : -7.075500 -0.3470001 16.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6416606E-02 2.0817420E-02 midg,1,midg; midg,igrid,midg 1.3669573E-02 2.0671762E-03 1,midg,midg; igrid,midg,midg -8.4521947E-03 3.3302315E-02 gauss-seidel spectral radius is 0.9985811 estimated iterations to convergence 210 setup time was (sec) 0.6000000 now iterating at: 18:30:31 rms-change max change #iterations 4.090824 173.7682 at 10iterations 1.892370 60.52358 at 20iterations 0.8711020 27.88109 at 30iterations 0.4021974 13.70660 at 40iterations 0.1862769 5.969482 at 50iterations 8.6028084E-02 2.687131 at 60iterations 3.9783280E-02 1.209814 at 70iterations 1.8395966E-02 0.5685043 at 80iterations 8.4979869E-03 0.2733994 at 90iterations 3.9125159E-03 0.1291809 at 100iterations 1.8035388E-03 5.5468559E-02 at 110iterations 8.3627732E-04 2.9006958E-02 at 120iterations finished qdiffx linear iterations at : 18:30:38 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 8.3627732E-04 2.9006958E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 18:30:39 8.363u 0.239s 0:08.92 96.3% 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 18:30:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.810724 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): -31.49400 17.34300 ymin,ymax (A): -23.58000 22.88600 zmin,zma (A): -12.49200 44.50400 x,y,z range (A): 48.83700 46.46600 56.99600 scale (grids/A): 2.810724 object centre (A): -7.075500 -0.3470001 16.00600 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.80106 86.59840 89.53385 assigned negative charge : -387.4045 centred at (gu) : 82.35011 86.78700 89.01603 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 165015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20747 grid for indexing accessible points = 1.400000 m= 82572 mr = 121696 m= 27936 mr = 68526 m= 6169 mr = 22757 m= 853 mr = 4776 m= 46 mr = 621 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 31523 time to turn everything in is 0.9100000 number of dielectric boundary points 64193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19628 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) : 1.873816 object centre at (A) : -7.075500 -0.3470001 16.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1079342 0.2034491 midg,1,midg; midg,igrid,midg 0.1608449 1.1355986E-02 1,midg,midg; igrid,midg,midg -4.9867291E-02 0.4312404 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.180000 now iterating at: 18:30:40 rms-change max change #iterations 9.541828 383.4870 at 10iterations 5.446261 110.6300 at 20iterations 3.100914 65.97936 at 30iterations 1.766538 33.60513 at 40iterations 1.005825 18.99749 at 50iterations 0.5709214 10.98995 at 60iterations 0.3244965 5.994080 at 70iterations 0.1849509 3.451278 at 80iterations 0.1052764 1.977485 at 90iterations 5.9756603E-02 1.179859 at 100iterations 3.3992898E-02 0.7106824 at 110iterations 1.9337464E-02 0.3948250 at 120iterations 1.0983824E-02 0.2141943 at 130iterations 6.2633078E-03 0.1153023 at 140iterations 3.5664709E-03 7.0863724E-02 at 150iterations 2.0241961E-03 4.0199280E-02 at 160iterations 1.1567130E-03 2.1789551E-02 at 170iterations 6.5513671E-04 1.3185501E-02 at 180iterations finished qdiffx linear iterations at : 18:30:53 total time elapsed so far: 13.79000 # loops : 180 mean,max change (kT/e) : 6.5513671E-04 1.3185501E-02 energy calculations done at 13.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.91000 DelPhi exited at 18:30:53 13.916u 0.268s 0:14.48 97.8% 0+0k 0+0io 0pf+0w