Sun Oct 9 14:10:51 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 Sun Oct 9 2011 at 14:10:51 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 = 2671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5747405 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): 0.1520001 51.51000 ymin,ymax (A): -12.38100 38.67400 zmin,zma (A): -15.10500 46.83600 x,y,z range (A): 51.35800 51.05500 61.94100 scale (grids/A): 0.5747405 object centre (A): 25.83100 13.14650 15.86550 number of atom coordinates read : 2671 total number of charged atoms : 2532 net assigned charge : 10.00002 assigned positive charge : 405.2206 centred at (gu) : 89.62316 91.68130 88.41246 assigned negative charge : -395.2216 centred at (gu) : 89.56074 91.53943 88.48389 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5826 nv = 96 ne = 84 npr = 52616 no. pairs analyzed = 52616 no. exposed pairs = 3470 no. arc points = 24582 no. surface atoms = 1164 nbur = 1507 mkacc time = 8.9999996E-02 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 = 1.512000 m= 284 mr = 2984 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2572 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7464 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2188151E-09 4.1477924E-10 midg,1,midg; midg,igrid,midg -3.8341322E-10 5.9992571E-09 1,midg,midg; igrid,midg,midg 7.8061968E-10 2.5280287E-09 gauss-seidel spectral radius is 0.9843538 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 14:10:51 rms-change max change #iterations 8.8591412E-02 16.31232 at 10iterations 6.6699991E-03 1.104303 at 20iterations 5.1316299E-04 8.7898254E-02 at 30iterations 3.9207374E-05 7.1406364E-03 at 40iterations 3.1318302E-06 5.2070618E-04 at 50iterations finished qdiffx linear iterations at : 14:10:54 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 3.1318302E-06 5.2070618E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:10:54 3.443u 0.178s 0:03.88 93.0% 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 14:10:55 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 = 2671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.724221 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): 0.1520001 51.51000 ymin,ymax (A): -12.38100 38.67400 zmin,zma (A): -15.10500 46.83600 x,y,z range (A): 51.35800 51.05500 61.94100 scale (grids/A): 1.724221 object centre (A): 25.83100 13.14650 15.86550 number of atom coordinates read : 2671 total number of charged atoms : 2532 net assigned charge : 10.00002 assigned positive charge : 405.2206 centred at (gu) : 88.86906 95.04311 85.23695 assigned negative charge : -395.2216 centred at (gu) : 88.68209 94.61821 85.45145 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24582 grid for indexing accessible points = 1.400000 m= 20430 mr = 42568 m= 2261 mr = 13894 m= 89 mr = 1046 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 28852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19596 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) : 0.5747405 object centre at (A) : 25.83100 13.14650 15.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5180098E-02 1.6934793E-02 midg,1,midg; midg,igrid,midg 4.2530424E-03 2.0094223E-02 1,midg,midg; igrid,midg,midg -1.0802083E-02 8.7162061E-03 gauss-seidel spectral radius is 0.9983512 estimated iterations to convergence 195 setup time was (sec) 0.5400000 now iterating at: 14:10:55 rms-change max change #iterations 3.470611 161.3422 at 10iterations 1.499366 56.88274 at 20iterations 0.6543556 25.57536 at 30iterations 0.2832682 10.12050 at 40iterations 0.1231226 4.748702 at 50iterations 5.3600356E-02 1.756603 at 60iterations 2.3174457E-02 0.9136047 at 70iterations 1.0092977E-02 0.4548435 at 80iterations 4.3851454E-03 0.1534939 at 90iterations 1.9108278E-03 6.9690704E-02 at 100iterations 8.3047833E-04 3.1555176E-02 at 110iterations 3.5987480E-04 1.2031555E-02 at 120iterations finished qdiffx linear iterations at : 14:11:02 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 3.5987480E-04 1.2031555E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:11:03 7.810u 0.202s 0:08.32 96.2% 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 Sun Oct 9 2011 at 14:11:03 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 = 2671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.586332 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): 0.1520001 51.51000 ymin,ymax (A): -12.38100 38.67400 zmin,zma (A): -15.10500 46.83600 x,y,z range (A): 51.35800 51.05500 61.94100 scale (grids/A): 2.586332 object centre (A): 25.83100 13.14650 15.86550 number of atom coordinates read : 2671 total number of charged atoms : 2532 net assigned charge : 10.00002 assigned positive charge : 405.2206 centred at (gu) : 88.30338 97.56455 82.85526 assigned negative charge : -395.2216 centred at (gu) : 88.02302 96.92721 83.17712 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 147493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24582 grid for indexing accessible points = 1.400000 m= 68957 mr = 103833 m= 20793 mr = 54148 m= 3521 mr = 15570 m= 304 mr = 2184 m= 10 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 65204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20241 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) : 1.724221 object centre at (A) : 25.83100 13.14650 15.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.059937 0.2642549 midg,1,midg; midg,igrid,midg 6.3809738E-02 0.1640539 1,midg,midg; igrid,midg,midg -0.1362563 0.1228491 gauss-seidel spectral radius is 0.9991816 estimated iterations to convergence 276 setup time was (sec) 1.030000 now iterating at: 14:11:04 rms-change max change #iterations 8.829330 377.3480 at 10iterations 5.110269 177.7112 at 20iterations 2.920007 79.46171 at 30iterations 1.660971 36.06169 at 40iterations 0.9406493 20.76470 at 50iterations 0.5309400 11.80978 at 60iterations 0.2989907 6.695366 at 70iterations 0.1683276 3.819057 at 80iterations 9.4478890E-02 2.083711 at 90iterations 5.2949328E-02 1.162087 at 100iterations 2.9696858E-02 0.6492157 at 110iterations 1.6633447E-02 0.3402596 at 120iterations 9.3180453E-03 0.1859074 at 130iterations 5.2082050E-03 0.1095457 at 140iterations 2.9052005E-03 5.8601379E-02 at 150iterations 1.6256567E-03 3.3348083E-02 at 160iterations 9.0846361E-04 1.8497467E-02 at 170iterations 5.0812581E-04 1.0520935E-02 at 180iterations finished qdiffx linear iterations at : 14:11:15 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 5.0812581E-04 1.0520935E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 14:11:16 12.462u 0.228s 0:12.99 97.6% 0+0k 0+0io 0pf+0w