Sun Oct 9 08:14:14 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 08:14:14 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3265 !!! WARNING: NAP 534 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5552003 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): 20.53200 79.09100 ymin,ymax (A): 1.976000 66.09700 zmin,zma (A): -23.33400 30.05300 x,y,z range (A): 58.55901 64.12100 53.38700 scale (grids/A): 0.5552003 object centre (A): 49.81150 34.03650 3.359500 number of atom coordinates read : 3265 total number of charged atoms : 3079 net assigned charge : 9.500031 assigned positive charge : 482.6530 centred at (gu) : 88.41348 91.37267 89.92638 assigned negative charge : -473.1543 centred at (gu) : 88.38940 91.38107 89.98164 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6580 nv = 96 ne = 84 npr = 65709 no. pairs analyzed = 65709 no. exposed pairs = 4143 no. arc points = 29943 no. surface atoms = 1376 nbur = 1889 mkacc time = 0.1600000 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= 280 mr = 3423 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3800000 number of dielectric boundary points 3421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2877 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8398 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4114061E-09 2.9054123E-10 midg,1,midg; midg,igrid,midg 6.7131761E-10 1.0543156E-09 1,midg,midg; igrid,midg,midg 8.7817648E-10 7.4316353E-10 gauss-seidel spectral radius is 0.9832933 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 08:14:15 rms-change max change #iterations 7.9923421E-02 12.14604 at 10iterations 5.7036085E-03 0.8469620 at 20iterations 4.4791974E-04 6.5143585E-02 at 30iterations 5.8010643E-05 8.3456039E-03 at 40iterations 1.0987052E-05 1.6422272E-03 at 50iterations finished qdiffx linear iterations at : 08:14:17 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.0987052E-05 1.6422272E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 08:14:18 3.223u 0.163s 0:03.68 91.8% 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 Sun Oct 9 2011 at 08:14:18 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3265 !!! WARNING: NAP 534 has a net charge of -2.0000 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: 1.665601 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): 20.53200 79.09100 ymin,ymax (A): 1.976000 66.09700 zmin,zma (A): -23.33400 30.05300 x,y,z range (A): 58.55901 64.12100 53.38700 scale (grids/A): 1.665601 object centre (A): 49.81150 34.03650 3.359500 number of atom coordinates read : 3265 total number of charged atoms : 3079 net assigned charge : 9.500031 assigned positive charge : 482.6530 centred at (gu) : 85.23965 94.11756 89.77845 assigned negative charge : -473.1543 centred at (gu) : 85.16784 94.14295 89.94480 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 23355 mr = 49313 m= 2557 mr = 16386 m= 71 mr = 1363 m= 1 mr = 12 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1014 time to turn everything in is 0.4900000 number of dielectric boundary points 31706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 23667 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) : 0.5552003 object centre at (A) : 49.81150 34.03650 3.359500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2451192E-03 7.1228170E-03 midg,1,midg; midg,igrid,midg 4.2964015E-03 1.0440351E-02 1,midg,midg; igrid,midg,midg 3.6214970E-02 1.7228972E-02 gauss-seidel spectral radius is 0.9982942 estimated iterations to convergence 192 setup time was (sec) 0.7700000 now iterating at: 08:14:19 rms-change max change #iterations 3.620897 226.3058 at 10iterations 1.548725 78.02567 at 20iterations 0.6586320 29.86843 at 30iterations 0.2823226 10.36909 at 40iterations 0.1209437 4.156536 at 50iterations 5.1866736E-02 1.819241 at 60iterations 2.2202833E-02 0.7375412 at 70iterations 9.4945207E-03 0.3376045 at 80iterations 4.0862788E-03 0.1392746 at 90iterations 1.7601491E-03 6.4837456E-02 at 100iterations 7.5749500E-04 2.4391174E-02 at 110iterations 3.2775427E-04 1.0923386E-02 at 120iterations finished qdiffx linear iterations at : 08:14:25 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 3.2775427E-04 1.0923386E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 08:14:25 7.009u 0.204s 0:07.47 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 08:14:25 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3265 !!! WARNING: NAP 534 has a net charge of -2.0000 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: 2.498401 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): 20.53200 79.09100 ymin,ymax (A): 1.976000 66.09700 zmin,zma (A): -23.33400 30.05300 x,y,z range (A): 58.55901 64.12100 53.38700 scale (grids/A): 2.498401 object centre (A): 49.81150 34.03650 3.359500 number of atom coordinates read : 3265 total number of charged atoms : 3079 net assigned charge : 9.500031 assigned positive charge : 482.6530 centred at (gu) : 82.85915 96.17609 89.66733 assigned negative charge : -473.1543 centred at (gu) : 82.75176 96.21437 89.91705 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 168978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 79092 mr = 120610 m= 24296 mr = 62928 m= 4176 mr = 18664 m= 313 mr = 2843 m= 4 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 3416 time to turn everything in is 1.230000 number of dielectric boundary points 71663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 24610 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) : 1.665601 object centre at (A) : 49.81150 34.03650 3.359500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6391221E-02 0.1774007 midg,1,midg; midg,igrid,midg 5.8111042E-02 0.2319481 1,midg,midg; igrid,midg,midg 0.6929759 0.2861921 gauss-seidel spectral radius is 0.9991763 estimated iterations to convergence 275 setup time was (sec) 1.550000 now iterating at: 08:14:27 rms-change max change #iterations 9.329223 378.2466 at 10iterations 5.323251 139.7343 at 20iterations 3.018015 72.89090 at 30iterations 1.708712 43.57963 at 40iterations 0.9612475 19.78652 at 50iterations 0.5398095 11.28150 at 60iterations 0.3029539 6.676697 at 70iterations 0.1697578 3.655914 at 80iterations 9.5073558E-02 2.089817 at 90iterations 5.3003497E-02 1.009535 at 100iterations 2.9554794E-02 0.5902596 at 110iterations 1.6525827E-02 0.3211060 at 120iterations 9.2309210E-03 0.1736603 at 130iterations 5.1534027E-03 9.9167347E-02 at 140iterations 2.8679445E-03 5.4721832E-02 at 150iterations 1.6061313E-03 3.3131838E-02 at 160iterations 8.9654676E-04 1.9252777E-02 at 170iterations 5.0213491E-04 9.2508793E-03 at 180iterations finished qdiffx linear iterations at : 08:14:38 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 5.0213491E-04 9.2508793E-03 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 08:14:38 12.258u 0.255s 0:12.78 97.8% 0+0k 0+0io 0pf+0w