Tue Oct 11 06:16:30 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 Tue Oct 11 2011 at 06:16:30 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.7152185 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): 3.506000 46.57000 ymin,ymax (A): 0.6100000 39.10200 zmin,zma (A): -2.453000 47.32200 x,y,z range (A): 43.06400 38.49200 49.77500 scale (grids/A): 0.7152185 object centre (A): 25.03800 19.85600 22.43450 number of atom coordinates read : 2057 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 90.28378 91.08860 90.39293 assigned negative charge : -304.5422 centred at (gu) : 90.46540 91.08741 90.42575 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7214 nv = 96 ne = 84 npr = 41447 no. pairs analyzed = 41447 no. exposed pairs = 2507 no. arc points = 17178 no. surface atoms = 847 nbur = 1210 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4226 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1633 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3828517E-08 5.6593358E-08 midg,1,midg; midg,igrid,midg 5.7942049E-08 8.8552262E-08 1,midg,midg; igrid,midg,midg 1.6441240E-07 -3.6566213E-08 gauss-seidel spectral radius is 0.9898048 estimated iterations to convergence 81 setup time was (sec) 0.5400000 now iterating at: 06:16:31 rms-change max change #iterations 0.2054337 28.89375 at 10iterations 2.6452985E-02 3.507744 at 20iterations 3.6101469E-03 0.5756264 at 30iterations 5.9537380E-04 8.4140778E-02 at 40iterations 1.4745117E-04 1.9227982E-02 at 50iterations finished qdiffx linear iterations at : 06:16:33 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.4745117E-04 1.9227982E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 06:16:34 3.187u 0.141s 0:03.64 91.2% 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 Tue Oct 11 2011 at 06:16:34 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.145655 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): 3.506000 46.57000 ymin,ymax (A): 0.6100000 39.10200 zmin,zma (A): -2.453000 47.32200 x,y,z range (A): 43.06400 38.49200 49.77500 scale (grids/A): 2.145655 object centre (A): 25.03800 19.85600 22.43450 number of atom coordinates read : 2057 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 90.85117 93.26588 91.17899 assigned negative charge : -304.5422 centred at (gu) : 91.39633 93.26220 91.27728 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17178 grid for indexing accessible points = 1.400000 m= 31677 mr = 54577 m= 6313 mr = 24336 m= 602 mr = 4309 m= 14 mr = 292 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 31276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15309 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) : 0.7152185 object centre at (A) : 25.03800 19.85600 22.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4533674E-02 7.3813125E-02 midg,1,midg; midg,igrid,midg 5.1564071E-03 3.4853160E-02 1,midg,midg; igrid,midg,midg 4.8388019E-02 8.6738244E-03 gauss-seidel spectral radius is 0.9988508 estimated iterations to convergence 233 setup time was (sec) 0.9100000 now iterating at: 06:16:35 rms-change max change #iterations 4.677842 191.3692 at 10iterations 2.333640 81.48732 at 20iterations 1.171692 35.51472 at 30iterations 0.5821300 17.01339 at 40iterations 0.2928245 9.041836 at 50iterations 0.1466109 4.402085 at 60iterations 7.3366441E-02 2.112999 at 70iterations 3.6724817E-02 1.178516 at 80iterations 1.8411569E-02 0.5464153 at 90iterations 9.2897899E-03 0.2617207 at 100iterations 4.6782685E-03 0.1441994 at 110iterations 2.4077934E-03 6.9648743E-02 at 120iterations finished qdiffx linear iterations at : 06:16:41 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 2.4077934E-03 6.9648743E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 06:16:41 7.011u 0.197s 0:07.52 95.7% 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 Tue Oct 11 2011 at 06:16:41 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.218483 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): 3.506000 46.57000 ymin,ymax (A): 0.6100000 39.10200 zmin,zma (A): -2.453000 47.32200 x,y,z range (A): 43.06400 38.49200 49.77500 scale (grids/A): 3.218483 object centre (A): 25.03800 19.85600 22.43450 number of atom coordinates read : 2057 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 91.27671 94.89896 91.76834 assigned negative charge : -304.5422 centred at (gu) : 92.09447 94.89326 91.91599 start vw surface at 0.1800000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 175816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17178 grid for indexing accessible points = 1.400000 m= 97600 mr = 131299 m= 40795 mr = 81934 m= 12077 mr = 33906 m= 2449 mr = 9418 m= 267 mr = 1789 m= 12 mr = 166 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 70499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15416 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) : 2.145655 object centre at (A) : 25.03800 19.85600 22.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3003326 0.9176710 midg,1,midg; midg,igrid,midg 5.8397430E-04 0.2658112 1,midg,midg; igrid,midg,midg 0.3805145 0.1507328 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 2.050000 now iterating at: 06:16:44 rms-change max change #iterations 10.35123 364.8278 at 10iterations 6.150188 145.6931 at 20iterations 3.648293 79.22870 at 30iterations 2.161467 47.19437 at 40iterations 1.275455 27.59915 at 50iterations 0.7511242 15.53333 at 60iterations 0.4424070 8.598782 at 70iterations 0.2604494 4.962143 at 80iterations 0.1528590 2.756781 at 90iterations 8.9919552E-02 1.626001 at 100iterations 5.3012509E-02 0.8843765 at 110iterations 3.1259034E-02 0.5458155 at 120iterations 1.8584782E-02 0.3302612 at 130iterations 1.1185753E-02 0.1968994 at 140iterations 6.8797041E-03 0.1295500 at 150iterations 4.3642716E-03 7.9303741E-02 at 160iterations 2.9051837E-03 5.2986145E-02 at 170iterations 2.0472412E-03 3.8249969E-02 at 180iterations finished qdiffx linear iterations at : 06:16:53 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 2.0472412E-03 3.8249969E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 06:16:54 11.685u 0.176s 0:12.35 95.9% 0+0k 0+0io 0pf+0w