Mon Oct 10 19:00:42 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 Mon Oct 10 2011 at 19:00:42 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 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: 0.6368515 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): 1.960000 56.74900 ymin,ymax (A): -18.89800 19.39100 zmin,zma (A): -26.10500 29.79500 x,y,z range (A): 54.78900 38.28900 55.90000 scale (grids/A): 0.6368515 object centre (A): 29.35450 0.2465000 1.845000 number of atom coordinates read : 2603 total number of charged atoms : 2466 net assigned charge : 1.000006 assigned positive charge : 386.8950 centred at (gu) : 89.28931 90.06159 90.25574 assigned negative charge : -385.8960 centred at (gu) : 89.26205 90.01411 90.29531 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7021 nv = 96 ne = 84 npr = 53055 no. pairs analyzed = 53055 no. exposed pairs = 3424 no. arc points = 23870 no. surface atoms = 1148 nbur = 1455 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 3678 m= 2 mr = 65 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 0.4000000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2339 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8510 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2555253E-09 -3.0359832E-09 midg,1,midg; midg,igrid,midg -3.6659875E-09 6.4747327E-09 1,midg,midg; igrid,midg,midg -1.8231699E-09 3.6531107E-09 gauss-seidel spectral radius is 0.9872308 estimated iterations to convergence 72 setup time was (sec) 0.7000000 now iterating at: 19:00:43 rms-change max change #iterations 0.1394119 20.99625 at 10iterations 1.3297573E-02 2.088825 at 20iterations 1.3446137E-03 0.2087984 at 30iterations 1.6365747E-04 2.2596359E-02 at 40iterations 3.7635840E-05 6.5745115E-03 at 50iterations finished qdiffx linear iterations at : 19:00:47 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 3.7635840E-05 6.5745115E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 19:00:47 4.276u 0.179s 0:04.98 89.1% 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 19:00:47 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 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: 1.910555 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): 1.960000 56.74900 ymin,ymax (A): -18.89800 19.39100 zmin,zma (A): -26.10500 29.79500 x,y,z range (A): 54.78900 38.28900 55.90000 scale (grids/A): 1.910555 object centre (A): 29.35450 0.2465000 1.845000 number of atom coordinates read : 2603 total number of charged atoms : 2466 net assigned charge : 1.000006 assigned positive charge : 386.8950 centred at (gu) : 87.86754 90.18431 90.76679 assigned negative charge : -385.8960 centred at (gu) : 87.78615 90.04235 90.88599 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 75648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23870 grid for indexing accessible points = 1.400000 m= 27783 mr = 51267 m= 5180 mr = 19978 m= 352 mr = 3247 m= 8 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 34336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 19393 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) : 0.6368515 object centre at (A) : 29.35450 0.2465000 1.845000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0273607E-02 -2.2443547E-03 midg,1,midg; midg,igrid,midg -2.0064134E-03 5.5468651E-03 1,midg,midg; igrid,midg,midg 1.7761629E-02 -1.6547251E-02 gauss-seidel spectral radius is 0.9986506 estimated iterations to convergence 216 setup time was (sec) 1.090000 now iterating at: 19:00:49 rms-change max change #iterations 4.258801 199.8398 at 10iterations 1.991805 66.56406 at 20iterations 0.9369020 29.29952 at 30iterations 0.4381138 15.22311 at 40iterations 0.2058790 6.512150 at 50iterations 9.7144231E-02 3.062107 at 60iterations 4.5632131E-02 1.408396 at 70iterations 2.1389635E-02 0.6990471 at 80iterations 1.0103548E-02 0.3007584 at 90iterations 4.7590490E-03 0.1442833 at 100iterations 2.2385102E-03 7.2372437E-02 at 110iterations 1.0534527E-03 3.7717819E-02 at 120iterations finished qdiffx linear iterations at : 19:00:57 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 1.0534527E-03 3.7717819E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 19:00:58 9.556u 0.231s 0:10.39 94.1% 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 19:00:58 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 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: 2.865832 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): 1.960000 56.74900 ymin,ymax (A): -18.89800 19.39100 zmin,zma (A): -26.10500 29.79500 x,y,z range (A): 54.78900 38.28900 55.90000 scale (grids/A): 2.865832 object centre (A): 29.35450 0.2465000 1.845000 number of atom coordinates read : 2603 total number of charged atoms : 2466 net assigned charge : 1.000006 assigned positive charge : 386.8950 centred at (gu) : 86.80115 90.27629 91.15010 assigned negative charge : -385.8960 centred at (gu) : 86.67933 90.06351 91.32880 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 174845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23870 grid for indexing accessible points = 1.400000 m= 87455 mr = 124626 m= 34289 mr = 70128 m= 9528 mr = 27224 m= 1580 mr = 7217 m= 112 mr = 1108 m= 0 mr = 53 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 77453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 19726 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) : 1.910555 object centre at (A) : 29.35450 0.2465000 1.845000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3597236 9.6961886E-02 midg,1,midg; midg,igrid,midg -1.9356532E-02 5.8647282E-03 1,midg,midg; igrid,midg,midg 0.1508973 -0.2980905 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 2.200000 now iterating at: 19:01:00 rms-change max change #iterations 10.29064 361.1757 at 10iterations 6.138544 181.6859 at 20iterations 3.638258 78.58916 at 30iterations 2.131810 40.38921 at 40iterations 1.251564 28.64867 at 50iterations 0.7289616 13.32460 at 60iterations 0.4249901 8.097875 at 70iterations 0.2471311 5.293549 at 80iterations 0.1433713 2.986675 at 90iterations 8.2958646E-02 1.812340 at 100iterations 4.8041981E-02 0.9401560 at 110iterations 2.7864194E-02 0.5407829 at 120iterations 1.6150147E-02 0.3243332 at 130iterations 9.3673877E-03 0.1738949 at 140iterations 5.4454673E-03 0.1012591 at 150iterations 3.2016286E-03 5.7262421E-02 at 160iterations 1.9086071E-03 3.7265062E-02 at 170iterations 1.1643920E-03 2.1621585E-02 at 180iterations finished qdiffx linear iterations at : 19:01:14 total time elapsed so far: 15.91000 # loops : 180 mean,max change (kT/e) : 1.1643920E-03 2.1621585E-02 energy calculations done at 15.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.13000 DelPhi exited at 19:01:15 16.134u 0.254s 0:16.87 97.0% 0+0k 0+0io 0pf+0w