Sun Oct 9 07:45:42 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 07:45:42 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 0.5488660 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): -3.957000 42.17500 ymin,ymax (A): 35.81600 89.04300 zmin,zma (A): -3.040000 61.82100 x,y,z range (A): 46.13200 53.22700 64.86100 scale (grids/A): 0.5488660 object centre (A): 19.10900 62.42950 29.39050 number of atom coordinates read : 2550 total number of charged atoms : 2403 net assigned charge : -12.49998 assigned positive charge : 381.5678 centred at (gu) : 90.42377 88.85460 89.65137 assigned negative charge : -394.0683 centred at (gu) : 90.58229 88.52798 89.62260 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5122 nv = 96 ne = 84 npr = 51058 no. pairs analyzed = 51058 no. exposed pairs = 3525 no. arc points = 25306 no. surface atoms = 1188 nbur = 1362 mkacc time = 0.1100000 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 = 1.540000 m= 197 mr = 2426 m= 0 mr = 12 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2511 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1101333E-09 -5.9360994E-10 midg,1,midg; midg,igrid,midg -4.0694346E-09 9.0922292E-10 1,midg,midg; igrid,midg,midg 1.6248715E-10 -2.0971045E-09 gauss-seidel spectral radius is 0.9828588 estimated iterations to convergence 63 setup time was (sec) 0.5200000 now iterating at: 07:45:43 rms-change max change #iterations 6.8067260E-02 13.56841 at 10iterations 4.4075502E-03 0.7496796 at 20iterations 2.9911721E-04 6.0992241E-02 at 30iterations 2.1010128E-05 3.4065247E-03 at 40iterations 1.5596310E-06 2.8800964E-04 at 50iterations finished qdiffx linear iterations at : 07:45:46 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.5596310E-06 2.8800964E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 07:45:46 3.362u 0.184s 0:03.81 92.9% 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 07:45:46 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 1.646598 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): -3.957000 42.17500 ymin,ymax (A): 35.81600 89.04300 zmin,zma (A): -3.040000 61.82100 x,y,z range (A): 46.13200 53.22700 64.86100 scale (grids/A): 1.646598 object centre (A): 19.10900 62.42950 29.39050 number of atom coordinates read : 2550 total number of charged atoms : 2403 net assigned charge : -12.49998 assigned positive charge : 381.5678 centred at (gu) : 91.27083 86.56318 88.95383 assigned negative charge : -394.0683 centred at (gu) : 91.74654 85.58376 88.86745 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 55974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25306 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16737 mr = 35772 m= 1584 mr = 11268 m= 35 mr = 686 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.4300000 number of dielectric boundary points 26600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18439 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) : 0.5488660 object centre at (A) : 19.10900 62.42950 29.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5762567E-02 -6.4439476E-03 midg,1,midg; midg,igrid,midg -2.7267592E-02 3.9451085E-03 1,midg,midg; igrid,midg,midg -3.4558289E-03 -1.5131164E-02 gauss-seidel spectral radius is 0.9981717 estimated iterations to convergence 186 setup time was (sec) 0.7300000 now iterating at: 07:45:47 rms-change max change #iterations 3.127251 166.0996 at 10iterations 1.299808 54.10117 at 20iterations 0.5377876 23.87012 at 30iterations 0.2221942 8.610811 at 40iterations 9.2466988E-02 3.436320 at 50iterations 3.8393017E-02 1.468845 at 60iterations 1.5884256E-02 0.6126633 at 70iterations 6.6035055E-03 0.2848892 at 80iterations 2.7376087E-03 0.1062093 at 90iterations 1.1359064E-03 4.4008732E-02 at 100iterations 4.7223383E-04 1.8205643E-02 at 110iterations 1.9616343E-04 7.2200298E-03 at 120iterations finished qdiffx linear iterations at : 07:45:54 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.9616343E-04 7.2200298E-03 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 07:45:54 7.531u 0.219s 0:08.08 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 Sun Oct 9 2011 at 07:45:54 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 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: 2.469897 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): -3.957000 42.17500 ymin,ymax (A): 35.81600 89.04300 zmin,zma (A): -3.040000 61.82100 x,y,z range (A): 46.13200 53.22700 64.86100 scale (grids/A): 2.469897 object centre (A): 19.10900 62.42950 29.39050 number of atom coordinates read : 2550 total number of charged atoms : 2403 net assigned charge : -12.49998 assigned positive charge : 381.5678 centred at (gu) : 91.90608 84.84469 88.43051 assigned negative charge : -394.0683 centred at (gu) : 92.61965 83.37554 88.30101 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 129663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25306 grid for indexing accessible points = 1.400000 m= 58586 mr = 87805 m= 15684 mr = 45769 m= 2263 mr = 11373 m= 147 mr = 1381 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 744 time to turn everything in is 0.9600000 number of dielectric boundary points 59954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19197 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) : 1.646598 object centre at (A) : 19.10900 62.42950 29.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9479014 -0.1062596 midg,1,midg; midg,igrid,midg -0.3573804 7.7058055E-02 1,midg,midg; igrid,midg,midg -5.2114788E-02 -0.1941810 gauss-seidel spectral radius is 0.9991282 estimated iterations to convergence 268 setup time was (sec) 1.280000 now iterating at: 07:45:56 rms-change max change #iterations 8.205297 277.6917 at 10iterations 4.581732 159.1096 at 20iterations 2.563643 62.15066 at 30iterations 1.421456 39.76699 at 40iterations 0.7887043 19.97496 at 50iterations 0.4368625 9.294008 at 60iterations 0.2408385 5.372614 at 70iterations 0.1327684 3.279034 at 80iterations 7.3087528E-02 1.970323 at 90iterations 4.0117696E-02 0.9203732 at 100iterations 2.2032676E-02 0.5129362 at 110iterations 1.2101471E-02 0.2814856 at 120iterations 6.6307643E-03 0.1497307 at 130iterations 3.6281003E-03 8.3684444E-02 at 140iterations 1.9850438E-03 4.2650223E-02 at 150iterations 1.0899885E-03 2.8131962E-02 at 160iterations 5.9751514E-04 1.3529241E-02 at 170iterations 3.2683893E-04 8.0108643E-03 at 180iterations finished qdiffx linear iterations at : 07:46:06 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 3.2683893E-04 8.0108643E-03 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 07:46:07 11.905u 0.220s 0:12.38 97.8% 0+0k 0+0io 0pf+0w