Sun Oct 9 11:21:15 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 11:21:15 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 214 has a net charge of 0.5140 !!! WARNING: CME 445 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of 0.1000 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: 0.5432212 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): 9.527000 67.05400 ymin,ymax (A): -34.53200 31.00300 zmin,zma (A): -7.356000 45.23800 x,y,z range (A): 57.52700 65.53500 52.59400 scale (grids/A): 0.5432212 object centre (A): 38.29050 -1.764501 18.94100 number of atom coordinates read : 2760 total number of charged atoms : 2613 net assigned charge : 1.131014 assigned positive charge : 400.6635 centred at (gu) : 87.82548 91.15730 89.86815 assigned negative charge : -399.5338 centred at (gu) : 87.90099 91.22175 90.03980 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5454 nv = 96 ne = 84 npr = 54429 no. pairs analyzed = 54429 no. exposed pairs = 3869 no. arc points = 27293 no. surface atoms = 1292 nbur = 1468 mkacc time = 9.9999994E-02 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 = 1.596000 m= 221 mr = 2582 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2695 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7085 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8720543E-10 -8.5162533E-10 midg,1,midg; midg,igrid,midg 2.9884986E-10 -3.9097206E-10 1,midg,midg; igrid,midg,midg 7.9488460E-10 -2.0264114E-10 gauss-seidel spectral radius is 0.9825264 estimated iterations to convergence 62 setup time was (sec) 0.3800000 now iterating at: 11:21:16 rms-change max change #iterations 6.7272447E-02 12.21694 at 10iterations 4.4143046E-03 0.7033615 at 20iterations 2.9528173E-04 5.6149960E-02 at 30iterations 2.2570634E-05 4.1961670E-03 at 40iterations 2.7281772E-06 4.5537949E-04 at 50iterations finished qdiffx linear iterations at : 11:21:19 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.7281772E-06 4.5537949E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:21:19 3.388u 0.173s 0:03.93 90.3% 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 Sun Oct 9 2011 at 11:21:19 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 214 has a net charge of 0.5140 !!! WARNING: CME 445 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of 0.1000 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: 1.629663 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): 9.527000 67.05400 ymin,ymax (A): -34.53200 31.00300 zmin,zma (A): -7.356000 45.23800 x,y,z range (A): 57.52700 65.53500 52.59400 scale (grids/A): 1.629663 object centre (A): 38.29050 -1.764501 18.94100 number of atom coordinates read : 2760 total number of charged atoms : 2613 net assigned charge : 1.131014 assigned positive charge : 400.6635 centred at (gu) : 83.47572 93.47148 89.60377 assigned negative charge : -399.5338 centred at (gu) : 83.70290 93.66516 90.11928 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17627 mr = 39573 m= 1817 mr = 11398 m= 55 mr = 826 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.3000000 number of dielectric boundary points 28621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 280 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 20066 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) : 0.5432212 object centre at (A) : 38.29050 -1.764501 18.94100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2220184E-02 -1.5907668E-02 midg,1,midg; midg,igrid,midg 6.3254186E-03 -1.2696823E-02 1,midg,midg; igrid,midg,midg 8.4288437E-03 -8.3108228E-03 gauss-seidel spectral radius is 0.9981731 estimated iterations to convergence 186 setup time was (sec) 0.5200000 now iterating at: 11:21:20 rms-change max change #iterations 3.125356 142.7451 at 10iterations 1.296286 50.31883 at 20iterations 0.5370842 23.39562 at 30iterations 0.2235797 8.994003 at 40iterations 9.2357911E-02 3.615566 at 50iterations 3.8480140E-02 1.457748 at 60iterations 1.5969502E-02 0.6867065 at 70iterations 6.6415104E-03 0.2541335 at 80iterations 2.7583714E-03 0.1075478 at 90iterations 1.1461747E-03 4.3153763E-02 at 100iterations 4.7963127E-04 1.8817902E-02 at 110iterations 2.0014241E-04 7.1349144E-03 at 120iterations finished qdiffx linear iterations at : 11:21:27 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.0014241E-04 7.1349144E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 11:21:27 7.615u 0.201s 0:08.18 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 Sun Oct 9 2011 at 11:21:27 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 214 has a net charge of 0.5140 !!! WARNING: CME 445 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.444495 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): 9.527000 67.05400 ymin,ymax (A): -34.53200 31.00300 zmin,zma (A): -7.356000 45.23800 x,y,z range (A): 57.52700 65.53500 52.59400 scale (grids/A): 2.444495 object centre (A): 38.29050 -1.764501 18.94100 number of atom coordinates read : 2760 total number of charged atoms : 2613 net assigned charge : 1.131014 assigned positive charge : 400.6635 centred at (gu) : 80.21335 95.20683 89.40541 assigned negative charge : -399.5338 centred at (gu) : 80.55439 95.49788 90.17896 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 141424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61261 mr = 97460 m= 17077 mr = 46613 m= 2844 mr = 12292 m= 199 mr = 1747 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 990 time to turn everything in is 0.7400000 number of dielectric boundary points 64609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20877 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) : 1.629663 object centre at (A) : 38.29050 -1.764501 18.94100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1772559 -0.2186376 midg,1,midg; midg,igrid,midg 8.9874998E-02 -0.2871851 1,midg,midg; igrid,midg,midg 0.1293039 -0.1422076 gauss-seidel spectral radius is 0.9991348 estimated iterations to convergence 269 setup time was (sec) 0.9600000 now iterating at: 11:21:29 rms-change max change #iterations 8.205035 284.9788 at 10iterations 4.633499 109.7098 at 20iterations 2.602420 62.64246 at 30iterations 1.448828 33.90028 at 40iterations 0.8052777 18.26945 at 50iterations 0.4455925 9.734184 at 60iterations 0.2458303 5.518402 at 70iterations 0.1357525 3.021928 at 80iterations 7.4626505E-02 1.676587 at 90iterations 4.1049596E-02 0.9016557 at 100iterations 2.2552636E-02 0.4940548 at 110iterations 1.2403476E-02 0.2532759 at 120iterations 6.7984140E-03 0.1563101 at 130iterations 3.7375286E-03 8.4882736E-02 at 140iterations 2.0459418E-03 4.5219421E-02 at 150iterations 1.1253387E-03 2.4444580E-02 at 160iterations 6.1670184E-04 1.2590408E-02 at 170iterations 3.3928367E-04 7.4596405E-03 at 180iterations finished qdiffx linear iterations at : 11:21:40 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 3.3928367E-04 7.4596405E-03 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 11:21:40 12.188u 0.200s 0:12.68 97.6% 0+0k 0+0io 0pf+0w