Mon Oct 10 17:17:36 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 17:17:36 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5123186 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): -17.13200 37.26700 ymin,ymax (A): -30.70000 35.35900 zmin,zma (A): -3.924000 65.56400 x,y,z range (A): 54.39900 66.05901 69.48801 scale (grids/A): 0.5123186 object centre (A): 10.06750 2.329500 30.82000 number of atom coordinates read : 4846 total number of charged atoms : 4595 net assigned charge : 7.706045 assigned positive charge : 729.4122 centred at (gu) : 89.87376 90.31076 88.45201 assigned negative charge : -721.7109 centred at (gu) : 89.75008 90.33637 88.42651 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8071 nv = 96 ne = 84 npr = 97443 no. pairs analyzed = 97443 no. exposed pairs = 6307 no. arc points = 43537 no. surface atoms = 2111 nbur = 2735 mkacc time = 0.2400000 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 = 1.652000 m= 282 mr = 4089 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4235 ## 666 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10751 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9485813E-11 1.2854155E-10 midg,1,midg; midg,igrid,midg 1.7688569E-10 5.1298469E-11 1,midg,midg; igrid,midg,midg -2.4196722E-10 4.4702256E-10 gauss-seidel spectral radius is 0.9805232 estimated iterations to convergence 59 setup time was (sec) 0.7800000 now iterating at: 17:17:37 rms-change max change #iterations 7.0357405E-02 9.885515 at 10iterations 5.2627437E-03 0.8823967 at 20iterations 1.0637774E-03 0.1491852 at 30iterations 4.0302071E-04 5.3475857E-02 at 40iterations 1.6982683E-04 2.4355888E-02 at 50iterations finished qdiffx linear iterations at : 17:17:40 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.6982683E-04 2.4355888E-02 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 17:17:41 3.811u 0.226s 0:04.53 88.9% 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 17:17:41 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.536956 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): -17.13200 37.26700 ymin,ymax (A): -30.70000 35.35900 zmin,zma (A): -3.924000 65.56400 x,y,z range (A): 54.39900 66.05901 69.48801 scale (grids/A): 1.536956 object centre (A): 10.06750 2.329500 30.82000 number of atom coordinates read : 4846 total number of charged atoms : 4595 net assigned charge : 7.706045 assigned positive charge : 729.4122 centred at (gu) : 89.61976 90.93056 85.35453 assigned negative charge : -721.7109 centred at (gu) : 89.25011 91.00856 85.27925 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 91635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26106 mr = 62396 m= 2275 mr = 16969 m= 48 mr = 936 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 39761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 579 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 34555 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) : 0.5123186 object centre at (A) : 10.06750 2.329500 30.82000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4385889E-03 1.8775681E-02 midg,1,midg; midg,igrid,midg 2.6970662E-03 -1.0249774E-02 1,midg,midg; igrid,midg,midg -3.4054217E-04 1.2471384E-02 gauss-seidel spectral radius is 0.9981396 estimated iterations to convergence 184 setup time was (sec) 1.030000 now iterating at: 17:17:42 rms-change max change #iterations 3.827593 167.6112 at 10iterations 1.579012 48.77604 at 20iterations 0.6531151 19.72127 at 30iterations 0.2704778 8.583273 at 40iterations 0.1116450 3.509183 at 50iterations 4.6389040E-02 1.639637 at 60iterations 1.9189503E-02 0.6845989 at 70iterations 8.0206189E-03 0.2420969 at 80iterations 3.4113659E-03 0.1122990 at 90iterations 1.5005155E-03 4.6657562E-02 at 100iterations 7.2576135E-04 2.5259018E-02 at 110iterations 4.0313337E-04 1.2912393E-02 at 120iterations finished qdiffx linear iterations at : 17:17:49 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 4.0313337E-04 1.2912393E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 17:17:50 8.398u 0.226s 0:09.16 93.9% 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 17:17:50 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.305434 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): -17.13200 37.26700 ymin,ymax (A): -30.70000 35.35900 zmin,zma (A): -3.924000 65.56400 x,y,z range (A): 54.39900 66.05901 69.48801 scale (grids/A): 2.305434 object centre (A): 10.06750 2.329500 30.82000 number of atom coordinates read : 4846 total number of charged atoms : 4595 net assigned charge : 7.706045 assigned positive charge : 729.4122 centred at (gu) : 89.42918 91.39552 83.03146 assigned negative charge : -721.7109 centred at (gu) : 88.87510 91.51282 82.91880 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 213671 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94404 mr = 153829 m= 23078 mr = 72908 m= 3297 mr = 16031 m= 203 mr = 1987 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 89824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 36664 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) : 1.536956 object centre at (A) : 10.06750 2.329500 30.82000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1298589 0.4795448 midg,1,midg; midg,igrid,midg -6.6311926E-02 -0.2621599 1,midg,midg; igrid,midg,midg -7.7843093E-03 0.1818495 gauss-seidel spectral radius is 0.9991755 estimated iterations to convergence 275 setup time was (sec) 2.000000 now iterating at: 17:17:52 rms-change max change #iterations 10.38591 252.9650 at 10iterations 5.987103 130.1630 at 20iterations 3.430525 79.62146 at 30iterations 1.949802 42.67430 at 40iterations 1.102523 23.08201 at 50iterations 0.6235205 13.21239 at 60iterations 0.3506997 7.631195 at 70iterations 0.1969988 4.085464 at 80iterations 0.1106488 2.145045 at 90iterations 6.2009685E-02 1.178608 at 100iterations 3.4702837E-02 0.7042618 at 110iterations 1.9476971E-02 0.3702736 at 120iterations 1.0891309E-02 0.2018814 at 130iterations 6.1066658E-03 0.1231384 at 140iterations 3.4371314E-03 6.6211700E-02 at 150iterations 1.9441803E-03 3.9398193E-02 at 160iterations 1.1182453E-03 2.0830154E-02 at 170iterations 6.5794442E-04 1.4985561E-02 at 180iterations finished qdiffx linear iterations at : 17:18:04 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 6.5794442E-04 1.4985561E-02 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 17:18:05 14.016u 0.233s 0:14.57 97.7% 0+0k 0+0io 0pf+0w