Mon Oct 10 17:03:07 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 17:03:07 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4783 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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: 0.5129979 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): -17.37400 36.71700 ymin,ymax (A): -30.95500 33.93100 zmin,zma (A): -3.866000 65.53000 x,y,z range (A): 54.09100 64.88600 69.39600 scale (grids/A): 0.5129979 object centre (A): 9.671501 1.488000 30.83200 number of atom coordinates read : 4783 total number of charged atoms : 4533 net assigned charge : 6.706028 assigned positive charge : 717.9876 centred at (gu) : 90.08564 90.61951 88.36372 assigned negative charge : -711.2857 centred at (gu) : 89.97608 90.65553 88.33317 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8014 nv = 96 ne = 84 npr = 96583 no. pairs analyzed = 96583 no. exposed pairs = 6189 no. arc points = 42714 no. surface atoms = 2058 nbur = 2725 mkacc time = 0.2500000 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= 297 mr = 4101 m= 1 mr = 6 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 0.5100000 number of dielectric boundary points 4205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4105 ## 583 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 10571 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8262840E-11 1.2755567E-10 midg,1,midg; midg,igrid,midg 1.7870162E-10 4.4155985E-12 1,midg,midg; igrid,midg,midg -2.0442550E-10 4.2499163E-10 gauss-seidel spectral radius is 0.9805699 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 17:03:08 rms-change max change #iterations 7.0085913E-02 9.813957 at 10iterations 4.1316245E-03 0.6137962 at 20iterations 4.8473306E-04 6.8142653E-02 at 30iterations 1.6883711E-04 2.8111458E-02 at 40iterations 6.8014931E-05 1.1559486E-02 at 50iterations finished qdiffx linear iterations at : 17:03:11 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.8014931E-05 1.1559486E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 17:03:11 3.542u 0.151s 0:04.13 89.3% 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 17:03:11 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4783 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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: 1.538994 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): -17.37400 36.71700 ymin,ymax (A): -30.95500 33.93100 zmin,zma (A): -3.866000 65.53000 x,y,z range (A): 54.09100 64.88600 69.39600 scale (grids/A): 1.538994 object centre (A): 9.671501 1.488000 30.83200 number of atom coordinates read : 4783 total number of charged atoms : 4533 net assigned charge : 6.706028 assigned positive charge : 717.9876 centred at (gu) : 90.25583 91.85742 85.08959 assigned negative charge : -711.2857 centred at (gu) : 89.92782 91.96623 84.99907 start vw surface at 0.2500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 90742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42714 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25661 mr = 62053 m= 2219 mr = 16689 m= 51 mr = 919 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 229 time to turn everything in is 0.7200000 number of dielectric boundary points 39010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 577 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 34199 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) : 0.5129979 object centre at (A) : 9.671501 1.488000 30.83200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8745905E-03 2.1840975E-02 midg,1,midg; midg,igrid,midg 4.5454927E-04 -1.1260350E-02 1,midg,midg; igrid,midg,midg -1.5575358E-03 1.0219446E-02 gauss-seidel spectral radius is 0.9981374 estimated iterations to convergence 184 setup time was (sec) 1.010000 now iterating at: 17:03:13 rms-change max change #iterations 3.866097 163.6129 at 10iterations 1.588999 53.73413 at 20iterations 0.6552039 20.26470 at 30iterations 0.2704481 10.06961 at 40iterations 0.1116567 3.894594 at 50iterations 4.6271909E-02 1.547909 at 60iterations 1.9105649E-02 0.5575304 at 70iterations 7.8998636E-03 0.2527161 at 80iterations 3.3027062E-03 0.1016364 at 90iterations 1.4023777E-03 4.5835495E-02 at 100iterations 6.2227977E-04 1.9393444E-02 at 110iterations 3.0333592E-04 1.1129856E-02 at 120iterations finished qdiffx linear iterations at : 17:03:19 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.0333592E-04 1.1129856E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 17:03:22 7.747u 0.185s 0:10.59 74.7% 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 17:03:22 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4783 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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: 2.308491 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): -17.37400 36.71700 ymin,ymax (A): -30.95500 33.93100 zmin,zma (A): -3.866000 65.53000 x,y,z range (A): 54.09100 64.88600 69.39600 scale (grids/A): 2.308491 object centre (A): 9.671501 1.488000 30.83200 number of atom coordinates read : 4783 total number of charged atoms : 4533 net assigned charge : 6.706028 assigned positive charge : 717.9876 centred at (gu) : 90.38324 92.78582 82.63417 assigned negative charge : -711.2857 centred at (gu) : 89.89172 92.94924 82.49862 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 211778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42714 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92797 mr = 152833 m= 22572 mr = 71812 m= 3091 mr = 15749 m= 165 mr = 1799 m= 0 mr = 67 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 760 time to turn everything in is 1.590000 number of dielectric boundary points 88143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 36191 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) : 1.538994 object centre at (A) : 9.671501 1.488000 30.83200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1357044 0.5000299 midg,1,midg; midg,igrid,midg -0.1067711 -0.2774592 1,midg,midg; igrid,midg,midg -2.2238847E-02 0.1450713 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 274 setup time was (sec) 1.900000 now iterating at: 17:03:24 rms-change max change #iterations 10.40715 271.1008 at 10iterations 5.993759 141.9236 at 20iterations 3.431640 104.2712 at 30iterations 1.942323 43.92861 at 40iterations 1.100295 28.82195 at 50iterations 0.6206033 15.33233 at 60iterations 0.3495908 7.403476 at 70iterations 0.1960992 3.679172 at 80iterations 0.1098586 2.384916 at 90iterations 6.1468240E-02 1.221667 at 100iterations 3.4380712E-02 0.7679510 at 110iterations 1.9253841E-02 0.3716984 at 120iterations 1.0774948E-02 0.2220688 at 130iterations 6.0105058E-03 0.1139688 at 140iterations 3.3707463E-03 7.0030212E-02 at 150iterations 1.8933398E-03 3.4839153E-02 at 160iterations 1.0711973E-03 2.3493767E-02 at 170iterations 6.1409554E-04 1.2398720E-02 at 180iterations finished qdiffx linear iterations at : 17:03:36 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 6.1409554E-04 1.2398720E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 17:03:37 13.537u 0.225s 0:14.86 92.5% 0+0k 0+0io 0pf+0w