Sat Oct 8 17:26:38 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 Sat Oct 8 2011 at 17:26:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3753 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: 0.5530269 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): -1.932000 60.53100 ymin,ymax (A): -18.47100 44.41600 zmin,zma (A): -5.423000 58.95000 x,y,z range (A): 62.46300 62.88700 64.37300 scale (grids/A): 0.5530269 object centre (A): 29.29950 12.97250 26.76350 number of atom coordinates read : 3753 total number of charged atoms : 3603 net assigned charge : -7.999969 assigned positive charge : 565.3494 centred at (gu) : 88.84760 86.64857 90.49425 assigned negative charge : -573.3517 centred at (gu) : 88.90540 86.63953 90.49457 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7549 nv = 96 ne = 84 npr = 75719 no. pairs analyzed = 75719 no. exposed pairs = 4861 no. arc points = 34390 no. surface atoms = 1612 nbur = 2141 mkacc time = 0.2600000 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= 331 mr = 3909 m= 0 mr = 15 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 3956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3474 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 9856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7342664E-10 -7.3276596E-10 midg,1,midg; midg,igrid,midg -1.6898567E-09 -2.5358199E-10 1,midg,midg; igrid,midg,midg -1.5874383E-11 -9.7274577E-10 gauss-seidel spectral radius is 0.9832001 estimated iterations to convergence 63 setup time was (sec) 0.8200000 now iterating at: 17:26:39 rms-change max change #iterations 8.6620808E-02 15.87420 at 10iterations 6.1225062E-03 0.9005568 at 20iterations 5.2065100E-04 7.4104309E-02 at 30iterations 8.8104403E-05 1.6127586E-02 at 40iterations 2.3365630E-05 4.0330887E-03 at 50iterations finished qdiffx linear iterations at : 17:26:42 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 2.3365630E-05 4.0330887E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 17:26:43 4.628u 0.433s 0:05.35 94.3% 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 Sat Oct 8 2011 at 17:26:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3753 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: 1.659081 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): -1.932000 60.53100 ymin,ymax (A): -18.47100 44.41600 zmin,zma (A): -5.423000 58.95000 x,y,z range (A): 62.46300 62.88700 64.37300 scale (grids/A): 1.659081 object centre (A): 29.29950 12.97250 26.76350 number of atom coordinates read : 3753 total number of charged atoms : 3603 net assigned charge : -7.999969 assigned positive charge : 565.3494 centred at (gu) : 86.54178 79.94434 91.48129 assigned negative charge : -573.3517 centred at (gu) : 86.71574 79.91798 91.48317 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 83265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26479 mr = 56616 m= 2884 mr = 18110 m= 87 mr = 1317 m= 0 mr = 7 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.8700000 number of dielectric boundary points 36665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 27697 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) : 0.5530269 object centre at (A) : 29.29950 12.97250 26.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0674718E-04 -4.1353251E-03 midg,1,midg; midg,igrid,midg -2.6547004E-02 -7.6928632E-03 1,midg,midg; igrid,midg,midg -1.2270772E-02 -3.0470097E-02 gauss-seidel spectral radius is 0.9983170 estimated iterations to convergence 194 setup time was (sec) 1.220000 now iterating at: 17:26:45 rms-change max change #iterations 3.942476 180.0078 at 10iterations 1.696298 62.40506 at 20iterations 0.7299259 24.01273 at 30iterations 0.3145134 9.695868 at 40iterations 0.1355973 4.513768 at 50iterations 5.8311995E-02 1.936783 at 60iterations 2.5180012E-02 0.7866876 at 70iterations 1.0859489E-02 0.4140930 at 80iterations 4.7042486E-03 0.1593476 at 90iterations 2.0309994E-03 6.4785004E-02 at 100iterations 8.8798947E-04 3.0487061E-02 at 110iterations 3.9275375E-04 1.2081146E-02 at 120iterations finished qdiffx linear iterations at : 17:26:55 total time elapsed so far: 11.05000 # loops : 120 mean,max change (kT/e) : 3.9275375E-04 1.2081146E-02 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 17:26:55 11.274u 0.470s 0:12.08 97.1% 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 Sat Oct 8 2011 at 17:26:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3753 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: 2.488621 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): -1.932000 60.53100 ymin,ymax (A): -18.47100 44.41600 zmin,zma (A): -5.423000 58.95000 x,y,z range (A): 62.46300 62.88700 64.37300 scale (grids/A): 2.488621 object centre (A): 29.29950 12.97250 26.76350 number of atom coordinates read : 3753 total number of charged atoms : 3603 net assigned charge : -7.999969 assigned positive charge : 565.3494 centred at (gu) : 84.81247 74.91624 92.22182 assigned negative charge : -573.3517 centred at (gu) : 85.07363 74.87688 92.22470 start vw surface at 0.1900000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 193400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 90873 mr = 138698 m= 26288 mr = 71427 m= 4380 mr = 19504 m= 321 mr = 2706 m= 7 mr = 116 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 846 time to turn everything in is 2.150000 number of dielectric boundary points 82819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 28788 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) : 1.659081 object centre at (A) : 29.29950 12.97250 26.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9594507E-02 0.1468363 midg,1,midg; midg,igrid,midg -0.4199848 -9.8620787E-02 1,midg,midg; igrid,midg,midg -0.1872748 -0.5737502 gauss-seidel spectral radius is 0.9991950 estimated iterations to convergence 278 setup time was (sec) 2.530000 now iterating at: 17:26:58 rms-change max change #iterations 10.11352 291.6639 at 10iterations 5.811058 158.6636 at 20iterations 3.323167 74.42984 at 30iterations 1.888308 36.59790 at 40iterations 1.071588 20.01733 at 50iterations 0.6043973 12.63535 at 60iterations 0.3419751 7.724587 at 70iterations 0.1929206 3.798607 at 80iterations 0.1085815 2.099573 at 90iterations 6.0920451E-02 1.258000 at 100iterations 3.4302235E-02 0.6138983 at 110iterations 1.9293582E-02 0.3981543 at 120iterations 1.0842306E-02 0.1907201 at 130iterations 6.0935742E-03 0.1206813 at 140iterations 3.4216158E-03 7.4086189E-02 at 150iterations 1.9269278E-03 3.8344860E-02 at 160iterations 1.0861487E-03 1.9012451E-02 at 170iterations 6.1292120E-04 1.1820316E-02 at 180iterations finished qdiffx linear iterations at : 17:27:18 total time elapsed so far: 21.94000 # loops : 180 mean,max change (kT/e) : 6.1292120E-04 1.1820316E-02 energy calculations done at 21.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.16000 DelPhi exited at 17:27:18 22.169u 0.505s 0:22.96 98.6% 0+0k 0+0io 0pf+0w