Mon Oct 10 19:33:20 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 19:33:20 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 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: 0.6381301 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): -5.138000 47.10000 ymin,ymax (A): -32.17000 23.61800 zmin,zma (A): -17.46300 37.06600 x,y,z range (A): 52.23800 55.78800 54.52900 scale (grids/A): 0.6381301 object centre (A): 20.98100 -4.276001 9.801501 number of atom coordinates read : 2764 total number of charged atoms : 2625 net assigned charge : 1.000028 assigned positive charge : 411.9566 centred at (gu) : 88.92940 91.47906 87.96837 assigned negative charge : -410.9577 centred at (gu) : 88.89761 91.53937 88.02377 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7658 nv = 96 ne = 84 npr = 55183 no. pairs analyzed = 55183 no. exposed pairs = 3851 no. arc points = 26572 no. surface atoms = 1292 nbur = 1472 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 3897 m= 0 mr = 50 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2569 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2173244E-08 -3.2665788E-09 midg,1,midg; midg,igrid,midg 6.0829870E-09 -7.9084534E-09 1,midg,midg; igrid,midg,midg -2.9681522E-09 4.0334052E-09 gauss-seidel spectral radius is 0.9872993 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 19:33:21 rms-change max change #iterations 0.1428223 20.41238 at 10iterations 1.4611186E-02 2.080244 at 20iterations 1.8655306E-03 0.2503872 at 30iterations 5.1976118E-04 6.1700821E-02 at 40iterations 2.0170165E-04 2.4045944E-02 at 50iterations finished qdiffx linear iterations at : 19:33:24 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.0170165E-04 2.4045944E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 19:33:24 3.427u 0.179s 0:04.11 87.3% 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 Mon Oct 10 2011 at 19:33:25 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 = 2764 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: 1.914390 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): -5.138000 47.10000 ymin,ymax (A): -32.17000 23.61800 zmin,zma (A): -17.46300 37.06600 x,y,z range (A): 52.23800 55.78800 54.52900 scale (grids/A): 1.914390 object centre (A): 20.98100 -4.276001 9.801501 number of atom coordinates read : 2764 total number of charged atoms : 2625 net assigned charge : 1.000028 assigned positive charge : 411.9566 centred at (gu) : 86.78773 94.43661 83.90446 assigned negative charge : -410.9577 centred at (gu) : 86.69255 94.61797 84.07097 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26572 grid for indexing accessible points = 1.400000 m= 29140 mr = 55098 m= 4717 mr = 20448 m= 270 mr = 2724 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 38009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20664 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) : 0.6381301 object centre at (A) : 20.98100 -4.276001 9.801501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0139693E-02 -9.7841611E-03 midg,1,midg; midg,igrid,midg 1.8249046E-02 -2.9864896E-02 1,midg,midg; igrid,midg,midg 7.9979915E-03 -4.8945262E-03 gauss-seidel spectral radius is 0.9986759 estimated iterations to convergence 218 setup time was (sec) 0.9900000 now iterating at: 19:33:26 rms-change max change #iterations 4.468369 204.8088 at 10iterations 2.110997 70.39665 at 20iterations 1.000775 35.04473 at 30iterations 0.4747272 13.95204 at 40iterations 0.2248681 6.948320 at 50iterations 0.1068939 3.167930 at 60iterations 5.0451554E-02 1.480156 at 70iterations 2.4104156E-02 0.7195301 at 80iterations 1.1498440E-02 0.3313751 at 90iterations 5.5053704E-03 0.1787376 at 100iterations 2.7061871E-03 8.1569672E-02 at 110iterations 1.3592612E-03 4.0339470E-02 at 120iterations finished qdiffx linear iterations at : 19:33:33 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 1.3592612E-03 4.0339470E-02 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 19:33:34 8.735u 0.250s 0:09.95 90.2% 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 19:33:35 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 = 2764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.871585 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): -5.138000 47.10000 ymin,ymax (A): -32.17000 23.61800 zmin,zma (A): -17.46300 37.06600 x,y,z range (A): 52.23800 55.78800 54.52900 scale (grids/A): 2.871585 object centre (A): 20.98100 -4.276001 9.801501 number of atom coordinates read : 2764 total number of charged atoms : 2625 net assigned charge : 1.000028 assigned positive charge : 411.9566 centred at (gu) : 85.18140 96.65482 80.85675 assigned negative charge : -410.9577 centred at (gu) : 85.03884 96.92693 81.10639 start vw surface at 0.2200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 190232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26572 grid for indexing accessible points = 1.400000 m= 93705 mr = 134687 m= 34432 mr = 74317 m= 8289 mr = 26600 m= 1115 mr = 5824 m= 51 mr = 627 m= 2 mr = 14 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 1.680000 number of dielectric boundary points 85757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 21000 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) : 1.914390 object centre at (A) : 20.98100 -4.276001 9.801501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5061856 -0.1997374 midg,1,midg; midg,igrid,midg 0.3579664 -0.2866325 1,midg,midg; igrid,midg,midg 0.1963912 -0.1647474 gauss-seidel spectral radius is 0.9992850 estimated iterations to convergence 295 setup time was (sec) 2.030000 now iterating at: 19:33:37 rms-change max change #iterations 10.56574 358.9700 at 10iterations 6.292953 137.0701 at 20iterations 3.727809 78.32432 at 30iterations 2.197204 42.05217 at 40iterations 1.292373 24.49318 at 50iterations 0.7568276 13.83585 at 60iterations 0.4432196 8.095018 at 70iterations 0.2592222 4.813934 at 80iterations 0.1511037 2.939079 at 90iterations 8.8202551E-02 1.574567 at 100iterations 5.1365156E-02 1.069475 at 110iterations 2.9951429E-02 0.5198402 at 120iterations 1.7488083E-02 0.2936802 at 130iterations 1.0250659E-02 0.2024364 at 140iterations 6.0249972E-03 0.1081810 at 150iterations 3.5896220E-03 6.5965652E-02 at 160iterations 2.1835621E-03 4.7086336E-02 at 170iterations 1.3790984E-03 2.6248932E-02 at 180iterations finished qdiffx linear iterations at : 19:33:49 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 1.3790984E-03 2.6248932E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 19:33:50 13.976u 0.279s 0:14.98 95.0% 0+0k 0+0io 0pf+0w