Mon Oct 10 14:00:25 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 14:00:25 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2135 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: ASL 106 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6788193 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): -17.37700 35.06700 ymin,ymax (A): -25.43000 21.64200 zmin,zma (A): -5.479000 39.06000 x,y,z range (A): 52.44400 47.07200 44.53900 scale (grids/A): 0.6788193 object centre (A): 8.844998 -1.894000 16.79050 number of atom coordinates read : 2135 total number of charged atoms : 1992 net assigned charge : -8.574971 assigned positive charge : 321.1519 centred at (gu) : 87.55951 91.48657 88.59659 assigned negative charge : -329.7270 centred at (gu) : 87.82413 91.55683 88.59516 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6453 nv = 96 ne = 84 npr = 45278 no. pairs analyzed = 45278 no. exposed pairs = 2625 no. arc points = 18552 no. surface atoms = 886 nbur = 1249 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3528 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.1700000 number of dielectric boundary points 3228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7524 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9176254E-08 -2.7812931E-08 midg,1,midg; midg,igrid,midg -1.3974262E-08 -7.5169048E-08 1,midg,midg; igrid,midg,midg 5.4438502E-08 -6.6980199E-08 gauss-seidel spectral radius is 0.9887027 estimated iterations to convergence 77 setup time was (sec) 0.3900000 now iterating at: 14:00:26 rms-change max change #iterations 0.1737527 26.57635 at 10iterations 1.9351711E-02 2.564075 at 20iterations 2.1523274E-03 0.2837176 at 30iterations 2.4653587E-04 3.4218788E-02 at 40iterations 2.7619471E-05 3.6697388E-03 at 50iterations finished qdiffx linear iterations at : 14:00:29 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 2.7619471E-05 3.6697388E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 14:00:30 3.717u 0.254s 0:04.94 80.1% 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 14:00:30 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2135 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: ASL 106 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: 2.036458 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): -17.37700 35.06700 ymin,ymax (A): -25.43000 21.64200 zmin,zma (A): -5.479000 39.06000 x,y,z range (A): 52.44400 47.07200 44.53900 scale (grids/A): 2.036458 object centre (A): 8.844998 -1.894000 16.79050 number of atom coordinates read : 2135 total number of charged atoms : 1992 net assigned charge : -8.574971 assigned positive charge : 321.1519 centred at (gu) : 82.67883 94.45972 85.78977 assigned negative charge : -329.7270 centred at (gu) : 83.47240 94.67048 85.78539 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18552 grid for indexing accessible points = 1.400000 m= 24655 mr = 46895 m= 4260 mr = 18174 m= 301 mr = 2747 m= 6 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 206 time to turn everything in is 0.3500000 number of dielectric boundary points 29883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15785 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) : 0.6788193 object centre at (A) : 8.844998 -1.894000 16.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2370382E-02 -2.9860690E-02 midg,1,midg; midg,igrid,midg 7.5661670E-04 -2.3694802E-02 1,midg,midg; igrid,midg,midg 9.1754897E-03 -6.7379139E-02 gauss-seidel spectral radius is 0.9987435 estimated iterations to convergence 223 setup time was (sec) 0.5800000 now iterating at: 14:00:31 rms-change max change #iterations 4.374818 172.3886 at 10iterations 2.113125 88.70782 at 20iterations 1.020280 31.28741 at 30iterations 0.4908752 15.87623 at 40iterations 0.2370831 7.651632 at 50iterations 0.1146330 3.674963 at 60iterations 5.5360757E-02 1.703360 at 70iterations 2.6650516E-02 0.9192761 at 80iterations 1.2860108E-02 0.4295549 at 90iterations 6.2226802E-03 0.1810246 at 100iterations 3.0005043E-03 9.7908020E-02 at 110iterations 1.4488195E-03 4.6177864E-02 at 120iterations finished qdiffx linear iterations at : 14:00:38 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 1.4488195E-03 4.6177864E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 14:00:39 8.157u 0.224s 0:08.71 96.0% 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 Mon Oct 10 2011 at 14:00:39 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2135 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: ASL 106 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: 3.054687 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): -17.37700 35.06700 ymin,ymax (A): -25.43000 21.64200 zmin,zma (A): -5.479000 39.06000 x,y,z range (A): 52.44400 47.07200 44.53900 scale (grids/A): 3.054687 object centre (A): 8.844998 -1.894000 16.79050 number of atom coordinates read : 2135 total number of charged atoms : 1992 net assigned charge : -8.574971 assigned positive charge : 321.1519 centred at (gu) : 79.01814 96.68959 83.68470 assigned negative charge : -329.7270 centred at (gu) : 80.20861 97.00564 83.67802 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 158300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18552 grid for indexing accessible points = 1.400000 m= 78939 mr = 113314 m= 29750 mr = 64428 m= 7757 mr = 24095 m= 1220 mr = 5886 m= 104 mr = 842 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 731 time to turn everything in is 0.9100000 number of dielectric boundary points 67460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 15932 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) : 2.036458 object centre at (A) : 8.844998 -1.894000 16.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1003813 -0.3285957 midg,1,midg; midg,igrid,midg 2.2961488E-02 -0.1630746 1,midg,midg; igrid,midg,midg 0.2732895 -0.5657914 gauss-seidel spectral radius is 0.9992796 estimated iterations to convergence 294 setup time was (sec) 1.170000 now iterating at: 14:00:40 rms-change max change #iterations 10.05883 349.4951 at 10iterations 5.872839 131.7765 at 20iterations 3.418886 61.89085 at 30iterations 1.986745 39.39740 at 40iterations 1.150992 22.64103 at 50iterations 0.6689222 13.23661 at 60iterations 0.3858774 6.903647 at 70iterations 0.2236083 4.227928 at 80iterations 0.1289828 2.364685 at 90iterations 7.4780710E-02 1.569230 at 100iterations 4.3159556E-02 0.7649722 at 110iterations 2.4991741E-02 0.5151482 at 120iterations 1.4422170E-02 0.2700467 at 130iterations 8.3496561E-03 0.1546135 at 140iterations 4.8290030E-03 8.6746216E-02 at 150iterations 2.7882063E-03 5.6398153E-02 at 160iterations 1.6114634E-03 3.1359971E-02 at 170iterations 9.3166652E-04 1.5712023E-02 at 180iterations finished qdiffx linear iterations at : 14:00:52 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 9.3166652E-04 1.5712023E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 14:00:53 12.824u 0.234s 0:14.41 90.5% 0+0k 0+0io 0pf+0w