Sun Oct 9 16:22:16 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 Sun Oct 9 2011 at 16:22:16 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3343 !!! WARNING: SEP 13 has a net charge of -0.4750 !!! WARNING: ASL 14 has a net charge of -0.1000 !!! WARNING: HIR 109 has a net charge of 0.5140 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: 0.5943436 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): -29.28300 27.78300 ymin,ymax (A): 3.663000 60.76800 zmin,zma (A): 289.0540 348.9520 x,y,z range (A): 57.06600 57.10500 59.89801 scale (grids/A): 0.5943436 object centre (A): -0.7500000 32.21550 319.0030 number of atom coordinates read : 3343 total number of charged atoms : 3198 net assigned charge : 2.939015 assigned positive charge : 524.5493 centred at (gu) : 90.77049 88.57229 90.20302 assigned negative charge : -521.6116 centred at (gu) : 90.85548 88.65255 90.28678 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8008 nv = 96 ne = 84 npr = 63411 no. pairs analyzed = 63411 no. exposed pairs = 5040 no. arc points = 35533 no. surface atoms = 1670 nbur = 1673 mkacc time = 0.1400000 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 = 1.456000 m= 374 mr = 3573 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3519 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2297765E-09 -2.5556075E-09 midg,1,midg; midg,igrid,midg 5.9793694E-09 -1.6320411E-09 1,midg,midg; igrid,midg,midg 3.7552961E-09 -2.9895428E-09 gauss-seidel spectral radius is 0.9854351 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 16:22:17 rms-change max change #iterations 0.1213258 22.84606 at 10iterations 1.0141750E-02 1.412659 at 20iterations 1.0158741E-03 0.1598587 at 30iterations 1.8466030E-04 1.8257141E-02 at 40iterations 4.9431186E-05 3.5638809E-03 at 50iterations finished qdiffx linear iterations at : 16:22:19 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 4.9431186E-05 3.5638809E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 16:22:20 3.225u 0.136s 0:03.64 92.0% 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 Sun Oct 9 2011 at 16:22:20 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3343 !!! WARNING: SEP 13 has a net charge of -0.4750 !!! WARNING: ASL 14 has a net charge of -0.1000 !!! WARNING: HIR 109 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.783031 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): -29.28300 27.78300 ymin,ymax (A): 3.663000 60.76800 zmin,zma (A): 289.0540 348.9520 x,y,z range (A): 57.06600 57.10500 59.89801 scale (grids/A): 1.783031 object centre (A): -0.7500000 32.21550 319.0030 number of atom coordinates read : 3343 total number of charged atoms : 3198 net assigned charge : 2.939015 assigned positive charge : 524.5493 centred at (gu) : 92.31034 85.71558 90.60839 assigned negative charge : -521.6116 centred at (gu) : 92.56602 85.95728 90.85984 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35533 grid for indexing accessible points = 1.400000 m= 26112 mr = 53149 m= 3065 mr = 16239 m= 115 mr = 1339 m= 7 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 370 time to turn everything in is 0.6000000 number of dielectric boundary points 44540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24935 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) : 0.5943436 object centre at (A) : -0.7500000 32.21550 319.0030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9241968E-02 -7.3362753E-02 midg,1,midg; midg,igrid,midg 2.0503335E-02 -2.0236533E-02 1,midg,midg; igrid,midg,midg 1.9449269E-02 1.3128783E-03 gauss-seidel spectral radius is 0.9985558 estimated iterations to convergence 209 setup time was (sec) 0.8800000 now iterating at: 16:22:21 rms-change max change #iterations 4.464567 157.9059 at 10iterations 2.026278 69.28671 at 20iterations 0.9271690 32.20335 at 30iterations 0.4236741 14.57346 at 40iterations 0.1938454 6.350758 at 50iterations 8.8445790E-02 2.842308 at 60iterations 4.0467750E-02 1.214009 at 70iterations 1.8540779E-02 0.5772004 at 80iterations 8.5145226E-03 0.2685537 at 90iterations 3.9190133E-03 0.1252146 at 100iterations 1.8028509E-03 5.4504395E-02 at 110iterations 8.3482417E-04 2.6590347E-02 at 120iterations finished qdiffx linear iterations at : 16:22:27 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 8.3482417E-04 2.6590347E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 16:22:28 7.345u 0.163s 0:07.78 96.4% 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 Sun Oct 9 2011 at 16:22:28 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3343 !!! WARNING: SEP 13 has a net charge of -0.4750 !!! WARNING: ASL 14 has a net charge of -0.1000 !!! WARNING: HIR 109 has a net charge of 0.5140 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: 2.674546 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): -29.28300 27.78300 ymin,ymax (A): 3.663000 60.76800 zmin,zma (A): 289.0540 348.9520 x,y,z range (A): 57.06600 57.10500 59.89801 scale (grids/A): 2.674546 object centre (A): -0.7500000 32.21550 319.0030 number of atom coordinates read : 3343 total number of charged atoms : 3198 net assigned charge : 2.939015 assigned positive charge : 524.5493 centred at (gu) : 93.46538 83.57309 90.91248 assigned negative charge : -521.6116 centred at (gu) : 93.84887 83.93583 91.28960 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 198963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35533 grid for indexing accessible points = 1.400000 m= 87733 mr = 131297 m= 25909 mr = 65045 m= 4743 mr = 17957 m= 456 mr = 2875 m= 24 mr = 185 m= 3 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8299999 no. cavity mid-points inaccessible to solvent = 1351 time to turn everything in is 1.460000 number of dielectric boundary points 100472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 25582 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) : 1.783031 object centre at (A) : -0.7500000 32.21550 319.0030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3006108 -1.206360 midg,1,midg; midg,igrid,midg 0.2357057 -0.3471908 1,midg,midg; igrid,midg,midg 0.2161710 -3.1529907E-02 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.760000 now iterating at: 16:22:30 rms-change max change #iterations 11.24220 359.6227 at 10iterations 6.866652 176.6637 at 20iterations 4.148395 92.93422 at 30iterations 2.485507 53.77814 at 40iterations 1.479108 33.50114 at 50iterations 0.8773310 16.76965 at 60iterations 0.5177062 10.44416 at 70iterations 0.3052859 6.273109 at 80iterations 0.1794318 3.426465 at 90iterations 0.1052751 1.992094 at 100iterations 6.1800521E-02 1.127480 at 110iterations 3.6133688E-02 0.7185698 at 120iterations 2.1126291E-02 0.3734310 at 130iterations 1.2335320E-02 0.2171907 at 140iterations 7.2066314E-03 0.1400032 at 150iterations 4.2142784E-03 8.3679199E-02 at 160iterations 2.4624241E-03 4.7706604E-02 at 170iterations 1.4396763E-03 2.3782253E-02 at 180iterations finished qdiffx linear iterations at : 16:22:40 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 1.4396763E-03 2.3782253E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 16:22:40 11.865u 0.185s 0:12.33 97.6% 0+0k 0+0io 0pf+0w