Sat Oct 15 15:18:05 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 15 2011 at 15:18:05 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 = 2917 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: 0.6548090 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): -4.398000 45.23300 ymin,ymax (A): -7.889000 42.71500 zmin,zma (A): -71.55800 -17.19100 x,y,z range (A): 49.63100 50.60400 54.36700 scale (grids/A): 0.6548090 object centre (A): 20.41750 17.41300 -44.37450 number of atom coordinates read : 2917 total number of charged atoms : 2770 net assigned charge : 6.000026 assigned positive charge : 441.4455 centred at (gu) : 88.94881 89.06496 87.76604 assigned negative charge : -435.4461 centred at (gu) : 89.09379 89.23952 87.82017 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7879 nv = 96 ne = 84 npr = 59528 no. pairs analyzed = 59528 no. exposed pairs = 4059 no. arc points = 27697 no. surface atoms = 1353 nbur = 1564 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 3750 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3900000 number of dielectric boundary points 4594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2637 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6170739E-08 1.3110995E-09 midg,1,midg; midg,igrid,midg 5.5201795E-08 -1.7945535E-08 1,midg,midg; igrid,midg,midg 4.9673822E-08 -1.2776364E-08 gauss-seidel spectral radius is 0.9879429 estimated iterations to convergence 74 setup time was (sec) 0.6800000 now iterating at: 15:18:06 rms-change max change #iterations 0.1657270 23.28161 at 10iterations 1.7371859E-02 2.278755 at 20iterations 2.0580289E-03 0.3600922 at 30iterations 4.0668438E-04 6.5168381E-02 at 40iterations 1.4091397E-04 1.8452644E-02 at 50iterations finished qdiffx linear iterations at : 15:18:10 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.4091397E-04 1.8452644E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 15:18:10 4.260u 0.263s 0:04.94 91.4% 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 15 2011 at 15:18:10 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 = 2917 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: 1.964427 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): -4.398000 45.23300 ymin,ymax (A): -7.889000 42.71500 zmin,zma (A): -71.55800 -17.19100 x,y,z range (A): 49.63100 50.60400 54.36700 scale (grids/A): 1.964427 object centre (A): 20.41750 17.41300 -44.37450 number of atom coordinates read : 2917 total number of charged atoms : 2770 net assigned charge : 6.000026 assigned positive charge : 441.4455 centred at (gu) : 86.84594 87.19448 83.29762 assigned negative charge : -435.4461 centred at (gu) : 87.28105 87.71820 83.46007 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27697 grid for indexing accessible points = 1.400000 m= 30751 mr = 52979 m= 6521 mr = 20943 m= 478 mr = 3953 m= 6 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 42293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 21863 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) : 0.6548090 object centre at (A) : 20.41750 17.41300 -44.37450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1366077 3.7063632E-02 midg,1,midg; midg,igrid,midg -8.9118083E-05 -1.6482364E-02 1,midg,midg; igrid,midg,midg 3.2589160E-02 -1.9515811E-02 gauss-seidel spectral radius is 0.9987522 estimated iterations to convergence 224 setup time was (sec) 1.100000 now iterating at: 15:18:12 rms-change max change #iterations 4.804204 203.9004 at 10iterations 2.321556 69.25764 at 20iterations 1.117484 38.42637 at 30iterations 0.5412529 16.12281 at 40iterations 0.2615535 8.054750 at 50iterations 0.1263922 3.952843 at 60iterations 6.1186105E-02 1.819688 at 70iterations 2.9687988E-02 0.9149590 at 80iterations 1.4414946E-02 0.4295359 at 90iterations 7.0340778E-03 0.1971598 at 100iterations 3.4470428E-03 0.1083722 at 110iterations 1.7194586E-03 4.8380852E-02 at 120iterations finished qdiffx linear iterations at : 15:18:21 total time elapsed so far: 9.920000 # loops : 120 mean,max change (kT/e) : 1.7194586E-03 4.8380852E-02 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.10000 DelPhi exited at 15:18:21 10.101u 0.361s 0:10.83 96.5% 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 15 2011 at 15:18:21 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 = 2917 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: 2.946640 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): -4.398000 45.23300 ymin,ymax (A): -7.889000 42.71500 zmin,zma (A): -71.55800 -17.19100 x,y,z range (A): 49.63100 50.60400 54.36700 scale (grids/A): 2.946640 object centre (A): 20.41750 17.41300 -44.37450 number of atom coordinates read : 2917 total number of charged atoms : 2770 net assigned charge : 6.000026 assigned positive charge : 441.4455 centred at (gu) : 85.26859 85.79148 79.94618 assigned negative charge : -435.4461 centred at (gu) : 85.92147 86.57716 80.18999 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 190058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27697 grid for indexing accessible points = 1.400000 m= 94327 mr = 129557 m= 39301 mr = 72641 m= 12109 mr = 30197 m= 2144 mr = 8819 m= 150 mr = 1375 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 95439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 22158 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) : 1.964427 object centre at (A) : 20.41750 17.41300 -44.37450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.502737 0.3614588 midg,1,midg; midg,igrid,midg -0.1965586 -8.5312396E-02 1,midg,midg; igrid,midg,midg 0.2023765 -0.1705710 gauss-seidel spectral radius is 0.9993062 estimated iterations to convergence 300 setup time was (sec) 2.440000 now iterating at: 15:18:24 rms-change max change #iterations 11.49255 357.9662 at 10iterations 6.989803 149.8966 at 20iterations 4.209221 94.39456 at 30iterations 2.529829 52.19165 at 40iterations 1.506984 31.38149 at 50iterations 0.8987679 17.98309 at 60iterations 0.5315555 9.525204 at 70iterations 0.3154059 5.674271 at 80iterations 0.1859188 3.407198 at 90iterations 0.1097215 1.868729 at 100iterations 6.4623356E-02 1.411432 at 110iterations 3.8007919E-02 0.6815720 at 120iterations 2.2364199E-02 0.4060001 at 130iterations 1.3144903E-02 0.2357521 at 140iterations 7.7153379E-03 0.1307316 at 150iterations 4.5376928E-03 7.7339172E-02 at 160iterations 2.6657488E-03 4.3025970E-02 at 170iterations 1.5719152E-03 2.6782990E-02 at 180iterations finished qdiffx linear iterations at : 15:18:39 total time elapsed so far: 17.53000 # loops : 180 mean,max change (kT/e) : 1.5719152E-03 2.6782990E-02 energy calculations done at 17.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 15:18:40 17.708u 0.368s 0:18.46 97.8% 0+0k 0+0io 0pf+0w