Sun Oct 9 13:25:17 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 Sun Oct 9 2011 at 13:25:17 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 0.6751631 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): -7.269000 44.32200 ymin,ymax (A): -13.90200 38.82600 zmin,zma (A): 1.511000 44.92200 x,y,z range (A): 51.59100 52.72800 43.41100 scale (grids/A): 0.6751631 object centre (A): 18.52650 12.46200 23.21650 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500025 assigned positive charge : 368.2111 centred at (gu) : 89.87226 90.59740 90.63635 assigned negative charge : -364.7115 centred at (gu) : 89.85154 90.77473 90.71592 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7327 nv = 96 ne = 84 npr = 48128 no. pairs analyzed = 48128 no. exposed pairs = 2998 no. arc points = 21132 no. surface atoms = 1002 nbur = 1391 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4042 m= 3 mr = 62 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 0.2600000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2035 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0993167E-08 -9.2175920E-09 midg,1,midg; midg,igrid,midg 5.4086986E-08 -4.0048590E-08 1,midg,midg; igrid,midg,midg 8.3861540E-09 1.8953841E-08 gauss-seidel spectral radius is 0.9886069 estimated iterations to convergence 76 setup time was (sec) 0.4700000 now iterating at: 13:25:18 rms-change max change #iterations 0.1799714 25.93790 at 10iterations 1.9997733E-02 3.027748 at 20iterations 2.4408109E-03 0.4048996 at 30iterations 3.9054989E-04 5.2692413E-02 at 40iterations 9.2551832E-05 1.3353348E-02 at 50iterations finished qdiffx linear iterations at : 13:25:20 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 9.2551832E-05 1.3353348E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 13:25:21 3.047u 0.139s 0:03.48 91.0% 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 13:25:21 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 2.025489 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): -7.269000 44.32200 ymin,ymax (A): -13.90200 38.82600 zmin,zma (A): 1.511000 44.92200 x,y,z range (A): 51.59100 52.72800 43.41100 scale (grids/A): 2.025489 object centre (A): 18.52650 12.46200 23.21650 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500025 assigned positive charge : 368.2111 centred at (gu) : 89.61623 91.79195 91.90872 assigned negative charge : -364.7115 centred at (gu) : 89.55452 92.32414 92.14747 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21132 grid for indexing accessible points = 1.400000 m= 29323 mr = 53760 m= 4990 mr = 21775 m= 450 mr = 3113 m= 9 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 33638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17814 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) : 0.6751631 object centre at (A) : 18.52650 12.46200 23.21650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0301649E-02 4.2476924E-03 midg,1,midg; midg,igrid,midg 1.3622897E-02 -6.1912127E-02 1,midg,midg; igrid,midg,midg 3.5893790E-02 4.0645264E-03 gauss-seidel spectral radius is 0.9987694 estimated iterations to convergence 226 setup time was (sec) 0.8000000 now iterating at: 13:25:22 rms-change max change #iterations 4.659325 206.6980 at 10iterations 2.253690 72.02688 at 20iterations 1.097872 36.71682 at 30iterations 0.5344006 15.82875 at 40iterations 0.2605417 8.548203 at 50iterations 0.1265422 3.825073 at 60iterations 6.1778206E-02 1.829559 at 70iterations 3.0012880E-02 0.8700180 at 80iterations 1.4709471E-02 0.4258566 at 90iterations 7.2060102E-03 0.2124863 at 100iterations 3.5478545E-03 0.1149960 at 110iterations 1.7595931E-03 5.9822798E-02 at 120iterations finished qdiffx linear iterations at : 13:25:28 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 1.7595931E-03 5.9822798E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 13:25:28 6.890u 0.154s 0:07.31 96.3% 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 Sun Oct 9 2011 at 13:25:28 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 3.038234 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): -7.269000 44.32200 ymin,ymax (A): -13.90200 38.82600 zmin,zma (A): 1.511000 44.92200 x,y,z range (A): 51.59100 52.72800 43.41100 scale (grids/A): 3.038234 object centre (A): 18.52650 12.46200 23.21650 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500025 assigned positive charge : 368.2111 centred at (gu) : 89.42435 92.68757 92.86288 assigned negative charge : -364.7115 centred at (gu) : 89.33165 93.48604 93.22122 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 179241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21132 grid for indexing accessible points = 1.400000 m= 93172 mr = 129971 m= 35274 mr = 76323 m= 9098 mr = 28392 m= 1817 mr = 6849 m= 218 mr = 1366 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 75801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 18008 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) : 2.025489 object centre at (A) : 18.52650 12.46200 23.21650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5035608 -6.2402353E-02 midg,1,midg; midg,igrid,midg 0.2791993 -0.7316616 1,midg,midg; igrid,midg,midg 0.3485807 -0.1981611 gauss-seidel spectral radius is 0.9992844 estimated iterations to convergence 295 setup time was (sec) 1.670000 now iterating at: 13:25:30 rms-change max change #iterations 10.68643 397.7382 at 10iterations 6.288264 145.9717 at 20iterations 3.702793 82.20831 at 30iterations 2.178726 38.87670 at 40iterations 1.277682 24.36758 at 50iterations 0.7449744 13.80493 at 60iterations 0.4358188 8.524853 at 70iterations 0.2543169 4.585861 at 80iterations 0.1479425 2.517233 at 90iterations 8.6268641E-02 1.685047 at 100iterations 5.0308727E-02 0.9898124 at 110iterations 2.9331217E-02 0.5172057 at 120iterations 1.7090062E-02 0.2960205 at 130iterations 1.0004362E-02 0.1668968 at 140iterations 5.8871051E-03 0.1051445 at 150iterations 3.5019761E-03 6.3934326E-02 at 160iterations 2.1296202E-03 4.0657043E-02 at 170iterations 1.3295277E-03 2.8373718E-02 at 180iterations finished qdiffx linear iterations at : 13:25:40 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 1.3295277E-03 2.8373718E-02 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 13:25:40 11.461u 0.174s 0:11.94 97.4% 0+0k 0+0io 0pf+0w