Wed Dec 21 14:22:12 PST 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 Wed Dec 21 2011 at 14:22:14 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5521606 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): -35.22200 11.77700 ymin,ymax (A): -2.7999997E-02 42.96300 zmin,zma (A): -3.574000 60.90000 x,y,z range (A): 46.99900 42.99100 64.47400 scale (grids/A): 0.5521606 object centre (A): -11.72250 21.46750 28.66300 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 294.1999 centred at (gu) : 89.99532 89.38125 89.51290 assigned negative charge : -292.2002 centred at (gu) : 89.91039 89.51893 89.51441 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 3981 nv = 96 ne = 84 npr = 40373 no. pairs analyzed = 40373 no. exposed pairs = 2409 no. arc points = 17225 no. surface atoms = 824 nbur = 1146 mkacc time = 0.1200000 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 = 1.568000 m= 134 mr = 2101 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1799 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8196102E-10 1.2961995E-10 midg,1,midg; midg,igrid,midg 1.0457606E-09 -5.2677096E-10 1,midg,midg; igrid,midg,midg -3.1806360E-10 6.1450961E-10 gauss-seidel spectral radius is 0.9830051 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 14:22:16 rms-change max change #iterations 6.2768593E-02 13.59529 at 10iterations 4.2220401E-03 0.7837601 at 20iterations 2.9104823E-04 6.9282532E-02 at 30iterations 1.9773444E-05 4.4403076E-03 at 40iterations 1.3989994E-06 2.8228760E-04 at 50iterations finished qdiffx linear iterations at : 14:22:20 total time elapsed so far: 4.870000 # loops : 50 mean,max change (kT/e) : 1.3989994E-06 2.8228760E-04 energy calculations done at 4.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.060000 DelPhi exited at 14:22:30 5.060u 0.322s 0:16.46 32.6% 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 Wed Dec 21 2011 at 14:22:32 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.656482 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): -35.22200 11.77700 ymin,ymax (A): -2.7999997E-02 42.96300 zmin,zma (A): -3.574000 60.90000 x,y,z range (A): 46.99900 42.99100 64.47400 scale (grids/A): 1.656482 object centre (A): -11.72250 21.46750 28.66300 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 294.1999 centred at (gu) : 89.98592 88.14363 88.53872 assigned negative charge : -292.2002 centred at (gu) : 89.73116 88.55694 88.54338 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 43621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17225 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14123 mr = 29542 m= 1534 mr = 10322 m= 46 mr = 824 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 692 time to turn everything in is 0.4400000 number of dielectric boundary points 18635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14136 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) : 0.5521606 object centre at (A) : -11.72250 21.46750 28.66300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9255141E-02 1.5061982E-02 midg,1,midg; midg,igrid,midg 6.7078992E-04 -5.5759330E-03 1,midg,midg; igrid,midg,midg -2.6251890E-03 -7.3021241E-05 gauss-seidel spectral radius is 0.9981134 estimated iterations to convergence 183 setup time was (sec) 0.7400000 now iterating at: 14:22:34 rms-change max change #iterations 2.732332 180.3702 at 10iterations 1.118015 50.07425 at 20iterations 0.4597951 19.49348 at 30iterations 0.1881545 7.605005 at 40iterations 7.7330351E-02 3.061661 at 50iterations 3.1599220E-02 1.341507 at 60iterations 1.2940210E-02 0.5391498 at 70iterations 5.3039198E-03 0.2391853 at 80iterations 2.1727451E-03 0.1163750 at 90iterations 8.9575618E-04 4.2093277E-02 at 100iterations 3.6531701E-04 1.7379761E-02 at 110iterations 1.4979996E-04 7.0014000E-03 at 120iterations finished qdiffx linear iterations at : 14:22:44 total time elapsed so far: 11.11000 # loops : 120 mean,max change (kT/e) : 1.4979996E-04 7.0014000E-03 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 14:22:50 11.310u 0.328s 0:17.93 64.8% 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 Wed Dec 21 2011 at 14:22:51 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.484723 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): -35.22200 11.77700 ymin,ymax (A): -2.7999997E-02 42.96300 zmin,zma (A): -3.574000 60.90000 x,y,z range (A): 46.99900 42.99100 64.47400 scale (grids/A): 2.484723 object centre (A): -11.72250 21.46750 28.66300 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 294.1999 centred at (gu) : 89.97878 87.21541 87.80804 assigned negative charge : -292.2002 centred at (gu) : 89.59669 87.83538 87.81503 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 101107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17225 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 48002 mr = 71648 m= 14530 mr = 39259 m= 2487 mr = 11504 m= 157 mr = 1738 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 2387 time to turn everything in is 0.9800000 number of dielectric boundary points 42062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 14691 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) : 1.656482 object centre at (A) : -11.72250 21.46750 28.66300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2368867 0.1572886 midg,1,midg; midg,igrid,midg -1.7638009E-02 -9.3558349E-02 1,midg,midg; igrid,midg,midg -4.6165254E-02 -2.4441617E-02 gauss-seidel spectral radius is 0.9990772 estimated iterations to convergence 260 setup time was (sec) 1.270000 now iterating at: 14:22:54 rms-change max change #iterations 6.912384 264.4986 at 10iterations 3.758784 117.3768 at 20iterations 2.032606 62.62096 at 30iterations 1.095100 29.63967 at 40iterations 0.5884727 14.33758 at 50iterations 0.3163278 8.019195 at 60iterations 0.1702454 3.921356 at 70iterations 9.1576427E-02 2.242186 at 80iterations 4.9110137E-02 1.154253 at 90iterations 2.6397437E-02 0.6745920 at 100iterations 1.4181649E-02 0.3578470 at 110iterations 7.6054465E-03 0.2110023 at 120iterations 4.0816204E-03 0.1031570 at 130iterations 2.1896651E-03 5.1098347E-02 at 140iterations 1.1743470E-03 3.0165672E-02 at 150iterations 6.3154276E-04 1.5380740E-02 at 160iterations 3.3897295E-04 8.1100464E-03 at 170iterations 1.8227992E-04 4.4498444E-03 at 180iterations finished qdiffx linear iterations at : 14:23:11 total time elapsed so far: 18.53000 # loops : 180 mean,max change (kT/e) : 1.8227992E-04 4.4498444E-03 energy calculations done at 18.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.73000 DelPhi exited at 14:23:12 18.728u 0.346s 0:20.63 92.3% 0+0k 0+0io 0pf+0w