Tue Oct 11 06:11:46 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 Tue Oct 11 2011 at 06:11:46 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 = 2061 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: 0.7223732 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): 0.8059999 46.23500 ymin,ymax (A): 0.6860000 40.29500 zmin,zma (A): -2.093000 47.18900 x,y,z range (A): 45.42900 39.60900 49.28200 scale (grids/A): 0.7223732 object centre (A): 23.52050 20.49050 22.54800 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 7.500009 assigned positive charge : 312.6270 centred at (gu) : 91.24170 90.61710 90.30734 assigned negative charge : -305.1272 centred at (gu) : 91.42654 90.59052 90.34852 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7306 nv = 96 ne = 84 npr = 41357 no. pairs analyzed = 41357 no. exposed pairs = 2505 no. arc points = 16968 no. surface atoms = 852 nbur = 1209 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 512 mr = 4254 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1589 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1191790E-07 6.7061627E-08 midg,1,midg; midg,igrid,midg 6.5538210E-08 1.2215587E-07 1,midg,midg; igrid,midg,midg 1.6793962E-07 -4.6189285E-08 gauss-seidel spectral radius is 0.9900047 estimated iterations to convergence 81 setup time was (sec) 0.5000000 now iterating at: 06:11:47 rms-change max change #iterations 0.2178965 32.89400 at 10iterations 2.8687986E-02 3.992088 at 20iterations 3.8733573E-03 0.4627943 at 30iterations 6.6279381E-04 8.2307816E-02 at 40iterations 1.7269957E-04 2.2935867E-02 at 50iterations finished qdiffx linear iterations at : 06:11:50 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.7269957E-04 2.2935867E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 06:11:50 3.257u 0.184s 0:03.86 88.8% 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 Tue Oct 11 2011 at 06:11:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 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: 2.167120 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): 0.8059999 46.23500 ymin,ymax (A): 0.6860000 40.29500 zmin,zma (A): -2.093000 47.18900 x,y,z range (A): 45.42900 39.60900 49.28200 scale (grids/A): 2.167120 object centre (A): 23.52050 20.49050 22.54800 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 7.500009 assigned positive charge : 312.6270 centred at (gu) : 93.72536 91.85136 90.92217 assigned negative charge : -305.1272 centred at (gu) : 94.27972 91.77149 91.04566 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16968 grid for indexing accessible points = 1.400000 m= 32012 mr = 55669 m= 6505 mr = 24570 m= 605 mr = 4401 m= 22 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15373 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) : 0.7223732 object centre at (A) : 23.52050 20.49050 22.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8774935E-02 7.0392750E-02 midg,1,midg; midg,igrid,midg 5.0025694E-03 3.9336570E-02 1,midg,midg; igrid,midg,midg 4.2315837E-02 3.8809122E-03 gauss-seidel spectral radius is 0.9988704 estimated iterations to convergence 235 setup time was (sec) 0.8700000 now iterating at: 06:11:51 rms-change max change #iterations 4.710592 190.1192 at 10iterations 2.354422 90.29582 at 20iterations 1.187476 35.94205 at 30iterations 0.5971617 18.54225 at 40iterations 0.3001149 8.704844 at 50iterations 0.1513887 4.658370 at 60iterations 7.5997703E-02 2.682999 at 70iterations 3.8451344E-02 1.128446 at 80iterations 1.9311933E-02 0.6174788 at 90iterations 9.8089762E-03 0.2724373 at 100iterations 5.0005238E-03 0.1564155 at 110iterations 2.5905932E-03 8.8577271E-02 at 120iterations finished qdiffx linear iterations at : 06:11:58 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.5905932E-03 8.8577271E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 06:11:59 7.580u 0.207s 0:08.38 92.8% 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 Tue Oct 11 2011 at 06:11:59 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 = 2061 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: 3.250680 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): 0.8059999 46.23500 ymin,ymax (A): 0.6860000 40.29500 zmin,zma (A): -2.093000 47.18900 x,y,z range (A): 45.42900 39.60900 49.28200 scale (grids/A): 3.250680 object centre (A): 23.52050 20.49050 22.54800 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 7.500009 assigned positive charge : 312.6270 centred at (gu) : 95.58794 92.77692 91.38328 assigned negative charge : -305.1272 centred at (gu) : 96.41957 92.65730 91.56854 start vw surface at 0.1500000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 179398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16968 grid for indexing accessible points = 1.400000 m= 98955 mr = 133717 m= 41300 mr = 82932 m= 12303 mr = 34291 m= 2648 mr = 9689 m= 297 mr = 1929 m= 11 mr = 189 m= 0 mr = 5 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 72160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15464 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) : 2.167120 object centre at (A) : 23.52050 20.49050 22.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4285749 0.8331587 midg,1,midg; midg,igrid,midg -1.2858758E-03 0.2985654 1,midg,midg; igrid,midg,midg 0.3026848 0.1485221 gauss-seidel spectral radius is 0.9993056 estimated iterations to convergence 299 setup time was (sec) 2.160000 now iterating at: 06:12:01 rms-change max change #iterations 10.42613 330.3880 at 10iterations 6.195091 133.2144 at 20iterations 3.672143 80.75984 at 30iterations 2.171983 42.48458 at 40iterations 1.283890 25.89036 at 50iterations 0.7558131 13.47501 at 60iterations 0.4459682 8.976921 at 70iterations 0.2621492 4.523497 at 80iterations 0.1548451 2.670629 at 90iterations 9.0794139E-02 1.649721 at 100iterations 5.3630605E-02 0.9487419 at 110iterations 3.1572640E-02 0.5213380 at 120iterations 1.8738126E-02 0.3414021 at 130iterations 1.1241583E-02 0.1855202 at 140iterations 6.8662269E-03 0.1181412 at 150iterations 4.3292847E-03 8.3102226E-02 at 160iterations 2.8649226E-03 5.0518036E-02 at 170iterations 2.0199746E-03 3.2089233E-02 at 180iterations finished qdiffx linear iterations at : 06:12:12 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 2.0199746E-03 3.2089233E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 06:12:12 12.823u 0.224s 0:13.80 94.4% 0+0k 0+0io 0pf+0w