Sun Oct 9 07:44:16 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 Sun Oct 9 2011 at 07:44:16 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 = 2551 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: 0.5482068 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): -4.422000 42.15300 ymin,ymax (A): 35.68900 88.95300 zmin,zma (A): -3.138000 61.80100 x,y,z range (A): 46.57500 53.26399 64.93900 scale (grids/A): 0.5482068 object centre (A): 18.86550 62.32100 29.33150 number of atom coordinates read : 2551 total number of charged atoms : 2406 net assigned charge : -12.49998 assigned positive charge : 381.8138 centred at (gu) : 90.62202 88.80469 89.72132 assigned negative charge : -394.3142 centred at (gu) : 90.78165 88.48109 89.68953 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5127 nv = 96 ne = 84 npr = 50914 no. pairs analyzed = 50914 no. exposed pairs = 3606 no. arc points = 25596 no. surface atoms = 1201 nbur = 1350 mkacc time = 0.1100000 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= 195 mr = 2399 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2601 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0813944E-09 -5.6688959E-10 midg,1,midg; midg,igrid,midg -3.9889136E-09 8.6598567E-10 1,midg,midg; igrid,midg,midg 1.5886562E-10 -2.1531326E-09 gauss-seidel spectral radius is 0.9828196 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 07:44:17 rms-change max change #iterations 6.7420192E-02 12.70610 at 10iterations 4.5035011E-03 0.8555679 at 20iterations 3.0353863E-04 5.3003311E-02 at 30iterations 2.3265253E-05 3.6621094E-03 at 40iterations 2.6798848E-06 4.6920776E-04 at 50iterations finished qdiffx linear iterations at : 07:44:19 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.6798848E-06 4.6920776E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:44:20 3.430u 0.198s 0:03.92 92.3% 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 07:44:20 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 = 2551 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.644620 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): -4.422000 42.15300 ymin,ymax (A): 35.68900 88.95300 zmin,zma (A): -3.138000 61.80100 x,y,z range (A): 46.57500 53.26399 64.93900 scale (grids/A): 1.644620 object centre (A): 18.86550 62.32100 29.33150 number of atom coordinates read : 2551 total number of charged atoms : 2406 net assigned charge : -12.49998 assigned positive charge : 381.8138 centred at (gu) : 91.86575 86.41341 89.16360 assigned negative charge : -394.3142 centred at (gu) : 92.34464 85.44292 89.06797 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 55923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25596 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16759 mr = 35543 m= 1531 mr = 11105 m= 31 mr = 700 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.4000000 number of dielectric boundary points 26896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 18463 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) : 0.5482068 object centre at (A) : 18.86550 62.32100 29.33150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4853015E-02 -4.8374310E-03 midg,1,midg; midg,igrid,midg -2.6839763E-02 3.8977845E-03 1,midg,midg; igrid,midg,midg -3.4858296E-03 -1.6382340E-02 gauss-seidel spectral radius is 0.9981683 estimated iterations to convergence 186 setup time was (sec) 0.7100000 now iterating at: 07:44:21 rms-change max change #iterations 3.125053 210.6861 at 10iterations 1.296974 54.50651 at 20iterations 0.5348720 21.38916 at 30iterations 0.2215203 8.670570 at 40iterations 9.2080720E-02 4.317424 at 50iterations 3.8225967E-02 1.511964 at 60iterations 1.5807148E-02 0.6641154 at 70iterations 6.5497621E-03 0.2806059 at 80iterations 2.7112677E-03 0.1084156 at 90iterations 1.1260619E-03 4.2883873E-02 at 100iterations 4.6676048E-04 1.8196106E-02 at 110iterations 1.9410632E-04 7.4996948E-03 at 120iterations finished qdiffx linear iterations at : 07:44:27 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.9410632E-04 7.4996948E-03 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 07:44:28 7.485u 0.239s 0:07.99 96.4% 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 07:44:28 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 = 2551 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: 2.466931 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): -4.422000 42.15300 ymin,ymax (A): 35.68900 88.95300 zmin,zma (A): -3.138000 61.80100 x,y,z range (A): 46.57500 53.26399 64.93900 scale (grids/A): 2.466931 object centre (A): 18.86550 62.32100 29.33150 number of atom coordinates read : 2551 total number of charged atoms : 2406 net assigned charge : -12.49998 assigned positive charge : 381.8138 centred at (gu) : 92.79839 84.62004 88.74528 assigned negative charge : -394.3142 centred at (gu) : 93.51682 83.16430 88.60189 start vw surface at 0.1400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 129185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25596 grid for indexing accessible points = 1.400000 m= 58578 mr = 87009 m= 15695 mr = 45392 m= 2170 mr = 11366 m= 156 mr = 1330 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 484 time to turn everything in is 0.9600000 number of dielectric boundary points 60609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19225 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) : 1.644620 object centre at (A) : 18.86550 62.32100 29.33150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8827618 -7.7317968E-02 midg,1,midg; midg,igrid,midg -0.3534780 7.3314756E-02 1,midg,midg; igrid,midg,midg -4.7818981E-02 -0.2067245 gauss-seidel spectral radius is 0.9991279 estimated iterations to convergence 268 setup time was (sec) 1.280000 now iterating at: 07:44:29 rms-change max change #iterations 8.240177 298.9160 at 10iterations 4.601700 135.2903 at 20iterations 2.580141 73.70547 at 30iterations 1.431118 34.41628 at 40iterations 0.7943653 19.36771 at 50iterations 0.4390336 10.03410 at 60iterations 0.2422449 5.493521 at 70iterations 0.1334403 3.196171 at 80iterations 7.3403984E-02 2.024908 at 90iterations 4.0271632E-02 0.9200878 at 100iterations 2.2156419E-02 0.5241270 at 110iterations 1.2168522E-02 0.3201756 at 120iterations 6.6664368E-03 0.1605549 at 130iterations 3.6501694E-03 8.1378341E-02 at 140iterations 1.9995808E-03 4.2993546E-02 at 150iterations 1.1004370E-03 2.3976803E-02 at 160iterations 6.0159090E-04 1.3877869E-02 at 170iterations 3.3049798E-04 7.4853897E-03 at 180iterations finished qdiffx linear iterations at : 07:44:40 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 3.3049798E-04 7.4853897E-03 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 07:44:40 12.069u 0.252s 0:12.61 97.6% 0+0k 0+0io 0pf+0w