Mon Oct 10 16:59:46 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 Mon Oct 10 2011 at 16:59:46 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 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: 0.5791066 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): -9.881000 40.41900 ymin,ymax (A): 50.43300 111.9070 zmin,zma (A): -10.92100 32.92300 x,y,z range (A): 50.30000 61.47400 43.84400 scale (grids/A): 0.5791066 object centre (A): 15.26900 81.17001 11.00100 number of atom coordinates read : 2750 total number of charged atoms : 2614 net assigned charge : 11.50002 assigned positive charge : 408.6114 centred at (gu) : 90.01418 88.69701 89.57511 assigned negative charge : -397.1124 centred at (gu) : 89.90126 88.76046 89.46618 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6084 nv = 96 ne = 84 npr = 55448 no. pairs analyzed = 55448 no. exposed pairs = 3415 no. arc points = 23823 no. surface atoms = 1154 nbur = 1596 mkacc time = 0.1600000 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= 280 mr = 3232 m= 0 mr = 22 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3500000 number of dielectric boundary points 3110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2481 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7779 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4345249E-10 4.0568620E-09 midg,1,midg; midg,igrid,midg 4.9118531E-09 9.1439178E-10 1,midg,midg; igrid,midg,midg 2.4405253E-10 4.5656980E-09 gauss-seidel spectral radius is 0.9845924 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 16:59:47 rms-change max change #iterations 9.2424527E-02 15.04028 at 10iterations 7.1600820E-03 1.251226 at 20iterations 5.5808650E-04 8.6704254E-02 at 30iterations 4.3785149E-05 6.6633224E-03 at 40iterations 3.3943988E-06 5.9127808E-04 at 50iterations finished qdiffx linear iterations at : 16:59:50 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 3.3943988E-06 5.9127808E-04 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 16:59:51 4.065u 0.264s 0:04.72 91.5% 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 Mon Oct 10 2011 at 16:59:51 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 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: 1.737320 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): -9.881000 40.41900 ymin,ymax (A): 50.43300 111.9070 zmin,zma (A): -10.92100 32.92300 x,y,z range (A): 50.30000 61.47400 43.84400 scale (grids/A): 1.737320 object centre (A): 15.26900 81.17001 11.00100 number of atom coordinates read : 2750 total number of charged atoms : 2614 net assigned charge : 11.50002 assigned positive charge : 408.6114 centred at (gu) : 90.04216 86.08994 88.72470 assigned negative charge : -397.1124 centred at (gu) : 89.70342 86.28116 88.39830 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 67007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23823 grid for indexing accessible points = 1.400000 m= 21949 mr = 45856 m= 2645 mr = 15415 m= 96 mr = 1449 m= 0 mr = 18 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1680 time to turn everything in is 0.5900000 number of dielectric boundary points 28959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 251 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20327 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) : 0.5791066 object centre at (A) : 15.26900 81.17001 11.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9997817E-03 1.4411515E-02 midg,1,midg; midg,igrid,midg 4.0126476E-02 4.4771968E-03 1,midg,midg; igrid,midg,midg 6.9365250E-03 2.7091224E-02 gauss-seidel spectral radius is 0.9983785 estimated iterations to convergence 197 setup time was (sec) 0.8800000 now iterating at: 16:59:52 rms-change max change #iterations 3.562719 152.8218 at 10iterations 1.550361 56.21483 at 20iterations 0.6791051 23.42163 at 30iterations 0.2967736 10.20790 at 40iterations 0.1298767 4.708946 at 50iterations 5.6677826E-02 1.999886 at 60iterations 2.4858760E-02 0.9238205 at 70iterations 1.0881218E-02 0.3732243 at 80iterations 4.7666626E-03 0.1694508 at 90iterations 2.0800072E-03 7.4676514E-02 at 100iterations 9.1554463E-04 3.4944534E-02 at 110iterations 4.0093338E-04 1.3705254E-02 at 120iterations finished qdiffx linear iterations at : 17:00:00 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 4.0093338E-04 1.3705254E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.250000 DelPhi exited at 17:00:01 9.249u 0.295s 0:09.86 96.6% 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 17:00:01 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 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: 2.605980 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): -9.881000 40.41900 ymin,ymax (A): 50.43300 111.9070 zmin,zma (A): -10.92100 32.92300 x,y,z range (A): 50.30000 61.47400 43.84400 scale (grids/A): 2.605980 object centre (A): 15.26900 81.17001 11.00100 number of atom coordinates read : 2750 total number of charged atoms : 2614 net assigned charge : 11.50002 assigned positive charge : 408.6114 centred at (gu) : 90.06313 84.13496 88.08695 assigned negative charge : -397.1124 centred at (gu) : 89.55505 84.42162 87.59731 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 155311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23823 grid for indexing accessible points = 1.400000 m= 73780 mr = 111823 m= 23263 mr = 58955 m= 4399 mr = 17823 m= 367 mr = 2977 m= 7 mr = 201 m= 0 mr = 1 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 5465 time to turn everything in is 1.480000 number of dielectric boundary points 65347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 20896 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) : 1.737320 object centre at (A) : 15.26900 81.17001 11.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0742143E-02 0.1777986 midg,1,midg; midg,igrid,midg 0.7081639 0.1511917 1,midg,midg; igrid,midg,midg 4.7933798E-02 0.3331066 gauss-seidel spectral radius is 0.9991940 estimated iterations to convergence 278 setup time was (sec) 1.810000 now iterating at: 17:00:03 rms-change max change #iterations 8.852520 301.6850 at 10iterations 5.083786 137.8432 at 20iterations 2.890584 90.75800 at 30iterations 1.635629 36.45863 at 40iterations 0.9251949 19.93930 at 50iterations 0.5227987 11.58655 at 60iterations 0.2941170 6.095816 at 70iterations 0.1650872 3.417243 at 80iterations 9.2849858E-02 2.366322 at 90iterations 5.2218463E-02 1.018929 at 100iterations 2.9253190E-02 0.6424932 at 110iterations 1.6423296E-02 0.3350754 at 120iterations 9.2229182E-03 0.2199326 at 130iterations 5.1674172E-03 0.1087341 at 140iterations 2.8969795E-03 5.7291985E-02 at 150iterations 1.6314144E-03 3.4897327E-02 at 160iterations 9.1434579E-04 1.9422770E-02 at 170iterations 5.1507191E-04 1.0007858E-02 at 180iterations finished qdiffx linear iterations at : 17:00:16 total time elapsed so far: 15.16000 # loops : 180 mean,max change (kT/e) : 5.1507191E-04 1.0007858E-02 energy calculations done at 15.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 17:00:17 15.337u 0.298s 0:16.34 95.5% 0+0k 0+0io 0pf+0w