Sun Oct 9 16:08:40 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+sph.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 = amb.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 16:08:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3061 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: 0.6345924 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): -15.54900 36.73800 ymin,ymax (A): 55.34800 107.8050 zmin,zma (A): -4.272000 51.82700 x,y,z range (A): 52.28700 52.45700 56.09900 scale (grids/A): 0.6345924 object centre (A): 10.59450 81.57650 23.77750 number of atom coordinates read : 3061 total number of charged atoms : 2917 net assigned charge : -4.499983 assigned positive charge : 451.4991 centred at (gu) : 90.36881 88.50386 91.41587 assigned negative charge : -456.0005 centred at (gu) : 90.40894 88.36674 91.45274 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8181 nv = 96 ne = 84 npr = 63186 no. pairs analyzed = 63186 no. exposed pairs = 3787 no. arc points = 26114 no. surface atoms = 1292 nbur = 1769 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4474 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2539 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2127210E-10 -1.2951396E-08 midg,1,midg; midg,igrid,midg -2.9924248E-08 7.6319271E-09 1,midg,midg; igrid,midg,midg -4.9191090E-10 -1.0755989E-08 gauss-seidel spectral radius is 0.9871759 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 16:08:41 rms-change max change #iterations 0.1549783 22.85239 at 10iterations 1.5039431E-02 1.906731 at 20iterations 1.4564958E-03 0.1823123 at 30iterations 1.4505077E-04 2.0118713E-02 at 40iterations 1.4885806E-05 1.9607544E-03 at 50iterations finished qdiffx linear iterations at : 16:08:44 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4885806E-05 1.9607544E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 16:08:44 3.351u 0.195s 0:03.85 91.9% 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 Sun Oct 9 2011 at 16:08:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3061 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: 1.903777 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): -15.54900 36.73800 ymin,ymax (A): 55.34800 107.8050 zmin,zma (A): -4.272000 51.82700 x,y,z range (A): 52.28700 52.45700 56.09900 scale (grids/A): 1.903777 object centre (A): 10.59450 81.57650 23.77750 number of atom coordinates read : 3061 total number of charged atoms : 2917 net assigned charge : -4.499983 assigned positive charge : 451.4991 centred at (gu) : 91.10578 85.51067 94.24683 assigned negative charge : -456.0005 centred at (gu) : 91.22665 85.09998 94.35796 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88661 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26114 grid for indexing accessible points = 1.400000 m= 32336 mr = 61988 m= 5453 mr = 23386 m= 351 mr = 3467 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 73 time to turn everything in is 0.6100000 number of dielectric boundary points 37852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22906 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) : 0.6345924 object centre at (A) : 10.59450 81.57650 23.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1940602E-02 2.3075305E-03 midg,1,midg; midg,igrid,midg -3.7594754E-02 -8.8112559E-03 1,midg,midg; igrid,midg,midg -3.8801916E-02 -3.0793002E-02 gauss-seidel spectral radius is 0.9986748 estimated iterations to convergence 218 setup time was (sec) 0.9100000 now iterating at: 16:08:45 rms-change max change #iterations 4.647058 206.2607 at 10iterations 2.193973 76.37316 at 20iterations 1.037404 30.27579 at 30iterations 0.4907358 15.58260 at 40iterations 0.2328030 6.943609 at 50iterations 0.1104956 3.406986 at 60iterations 5.2377485E-02 1.458414 at 70iterations 2.4761681E-02 0.7011635 at 80iterations 1.1727080E-02 0.3385468 at 90iterations 5.5647809E-03 0.1786375 at 100iterations 2.6334045E-03 7.4731827E-02 at 110iterations 1.2501929E-03 3.6293030E-02 at 120iterations finished qdiffx linear iterations at : 16:08:53 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 1.2501929E-03 3.6293030E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 16:08:54 8.711u 0.252s 0:09.23 97.0% 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 16:08:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3061 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.855666 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): -15.54900 36.73800 ymin,ymax (A): 55.34800 107.8050 zmin,zma (A): -4.272000 51.82700 x,y,z range (A): 52.28700 52.45700 56.09900 scale (grids/A): 2.855666 object centre (A): 10.59450 81.57650 23.77750 number of atom coordinates read : 3061 total number of charged atoms : 2917 net assigned charge : -4.499983 assigned positive charge : 451.4991 centred at (gu) : 91.65858 83.26591 96.37005 assigned negative charge : -456.0005 centred at (gu) : 91.83998 82.64995 96.53696 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 205159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26114 grid for indexing accessible points = 1.400000 m= 103292 mr = 150507 m= 38904 mr = 83706 m= 10093 mr = 30785 m= 1486 mr = 7560 m= 81 mr = 991 m= 0 mr = 29 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 1.580000 number of dielectric boundary points 85437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 23335 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) : 1.903777 object centre at (A) : 10.59450 81.57650 23.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5138740 7.5259060E-02 midg,1,midg; midg,igrid,midg -0.4003104 -0.2483165 1,midg,midg; igrid,midg,midg -0.5464606 -0.3598359 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 1.880000 now iterating at: 16:08:56 rms-change max change #iterations 10.89664 407.8207 at 10iterations 6.431094 150.4236 at 20iterations 3.758305 75.60130 at 30iterations 2.204179 44.59152 at 40iterations 1.288140 23.70760 at 50iterations 0.7500410 13.96853 at 60iterations 0.4369688 8.463468 at 70iterations 0.2538173 4.417312 at 80iterations 0.1476985 2.691566 at 90iterations 8.5892886E-02 1.698578 at 100iterations 4.9900386E-02 0.9742217 at 110iterations 2.8937083E-02 0.5261488 at 120iterations 1.6826930E-02 0.3011951 at 130iterations 9.7571379E-03 0.1651011 at 140iterations 5.6640306E-03 9.7087860E-02 at 150iterations 3.2821896E-03 5.6101441E-02 at 160iterations 1.9052882E-03 3.3679008E-02 at 170iterations 1.1099350E-03 2.0732880E-02 at 180iterations finished qdiffx linear iterations at : 16:09:07 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.1099350E-03 2.0732880E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 16:09:07 13.015u 0.246s 0:13.69 96.7% 0+0k 0+0io 0pf+0w