Mon Oct 10 14:40:44 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 14:40:44 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 0.5831381 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): -8.243999 52.80500 ymin,ymax (A): -16.09000 34.27800 zmin,zma (A): 77.64799 130.2890 x,y,z range (A): 61.04900 50.36800 52.64101 scale (grids/A): 0.5831381 object centre (A): 22.28050 9.094000 103.9685 number of atom coordinates read : 2729 total number of charged atoms : 2587 net assigned charge : -1.599990 assigned positive charge : 426.7654 centred at (gu) : 92.27202 89.82140 89.40742 assigned negative charge : -428.3663 centred at (gu) : 92.17781 89.92184 89.49618 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6245 nv = 96 ne = 84 npr = 53042 no. pairs analyzed = 53042 no. exposed pairs = 3771 no. arc points = 26274 no. surface atoms = 1271 nbur = 1458 mkacc time = 0.1000000 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= 312 mr = 3132 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8408358E-09 -2.2252586E-09 midg,1,midg; midg,igrid,midg 1.9447635E-09 -2.7199196E-09 1,midg,midg; igrid,midg,midg -1.5847930E-09 2.9900129E-09 gauss-seidel spectral radius is 0.9848052 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 14:40:45 rms-change max change #iterations 9.8753482E-02 15.70138 at 10iterations 7.8183869E-03 1.112816 at 20iterations 6.8880996E-04 0.1168327 at 30iterations 1.0443322E-04 2.2311211E-02 at 40iterations 2.7349986E-05 6.4048767E-03 at 50iterations finished qdiffx linear iterations at : 14:40:48 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.7349986E-05 6.4048767E-03 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 14:40:48 3.381u 0.158s 0:03.88 90.9% 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 14:40:48 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 1.749414 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): -8.243999 52.80500 ymin,ymax (A): -16.09000 34.27800 zmin,zma (A): 77.64799 130.2890 x,y,z range (A): 61.04900 50.36800 52.64101 scale (grids/A): 1.749414 object centre (A): 22.28050 9.094000 103.9685 number of atom coordinates read : 2729 total number of charged atoms : 2587 net assigned charge : -1.599990 assigned positive charge : 426.7654 centred at (gu) : 96.81529 89.46363 88.22180 assigned negative charge : -428.3663 centred at (gu) : 96.53324 89.76526 88.48822 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26274 grid for indexing accessible points = 1.400000 m= 22429 mr = 44674 m= 2796 mr = 15074 m= 111 mr = 1373 m= 1 mr = 7 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 0.3400000 number of dielectric boundary points 31631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20056 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) : 0.5831381 object centre at (A) : 22.28050 9.094000 103.9685 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0637997E-03 -2.7422434E-02 midg,1,midg; midg,igrid,midg 5.6575704E-03 -1.4828449E-02 1,midg,midg; igrid,midg,midg 1.9083569E-02 4.2248905E-02 gauss-seidel spectral radius is 0.9984121 estimated iterations to convergence 199 setup time was (sec) 0.5400000 now iterating at: 14:40:49 rms-change max change #iterations 3.794779 172.8971 at 10iterations 1.656762 67.94380 at 20iterations 0.7296847 27.19927 at 30iterations 0.3200644 10.46291 at 40iterations 0.1408886 5.137976 at 50iterations 6.2071551E-02 2.154253 at 60iterations 2.7399579E-02 0.9907696 at 70iterations 1.2068944E-02 0.4228706 at 80iterations 5.3401752E-03 0.1966190 at 90iterations 2.3614948E-03 7.7026367E-02 at 100iterations 1.0543325E-03 3.7425995E-02 at 110iterations 4.7336699E-04 1.5884697E-02 at 120iterations finished qdiffx linear iterations at : 14:40:56 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 4.7336699E-04 1.5884697E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 14:40:56 7.663u 0.207s 0:08.25 95.2% 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 14:40:56 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2729 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 2.624122 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): -8.243999 52.80500 ymin,ymax (A): -16.09000 34.27800 zmin,zma (A): 77.64799 130.2890 x,y,z range (A): 61.04900 50.36800 52.64101 scale (grids/A): 2.624122 object centre (A): 22.28050 9.094000 103.9685 number of atom coordinates read : 2729 total number of charged atoms : 2587 net assigned charge : -1.599990 assigned positive charge : 426.7654 centred at (gu) : 100.2228 89.19523 87.33263 assigned negative charge : -428.3663 centred at (gu) : 99.79972 89.64780 87.73231 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 156183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26274 grid for indexing accessible points = 1.400000 m= 74557 mr = 109661 m= 23970 mr = 57866 m= 4661 mr = 17781 m= 480 mr = 2985 m= 10 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 71315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20683 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) : 1.749414 object centre at (A) : 22.28050 9.094000 103.9685 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9572795E-02 -0.3796480 midg,1,midg; midg,igrid,midg 7.3150873E-02 -0.1467834 1,midg,midg; igrid,midg,midg 0.4753999 0.4791375 gauss-seidel spectral radius is 0.9992054 estimated iterations to convergence 280 setup time was (sec) 1.070000 now iterating at: 14:40:58 rms-change max change #iterations 9.538344 283.2722 at 10iterations 5.525154 125.1986 at 20iterations 3.165444 66.55889 at 30iterations 1.807990 37.47440 at 40iterations 1.027227 20.45070 at 50iterations 0.5830596 12.18019 at 60iterations 0.3301451 6.772319 at 70iterations 0.1867533 3.773033 at 80iterations 0.1055525 2.077179 at 90iterations 5.9489716E-02 1.261959 at 100iterations 3.3620987E-02 0.7699585 at 110iterations 1.8992288E-02 0.3859625 at 120iterations 1.0687332E-02 0.2117596 at 130iterations 6.0333335E-03 0.1244611 at 140iterations 3.3993265E-03 6.9973946E-02 at 150iterations 1.9249358E-03 3.9516449E-02 at 160iterations 1.0950060E-03 2.3260117E-02 at 170iterations 6.2518538E-04 1.2004852E-02 at 180iterations finished qdiffx linear iterations at : 14:41:09 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 6.2518538E-04 1.2004852E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 14:41:09 12.285u 0.213s 0:12.79 97.6% 0+0k 0+0io 0pf+0w