Mon Oct 10 14:37:14 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+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 Mon Oct 10 2011 at 14:37:14 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: ADP 651 has a net charge of -2.0000 !!! WARNING: MG6 652 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.4201036 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): -5.681000 48.70600 ymin,ymax (A): 16.10000 100.8410 zmin,zma (A): 14.75900 72.72600 x,y,z range (A): 54.38700 84.74100 57.96700 scale (grids/A): 0.4201036 object centre (A): 21.51250 58.47050 43.74250 number of atom coordinates read : 2667 total number of charged atoms : 2518 net assigned charge : -4.599990 assigned positive charge : 412.9636 centred at (gu) : 88.97482 96.77892 89.00453 assigned negative charge : -417.5643 centred at (gu) : 89.03838 96.72729 89.03928 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 2839 nv = 96 ne = 84 npr = 51732 no. pairs analyzed = 51732 no. exposed pairs = 3741 no. arc points = 26199 no. surface atoms = 1260 nbur = 1407 mkacc time = 9.0000004E-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 = 1.988000 m= 70 mr = 1199 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 0.1800000 number of dielectric boundary points 1710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 506 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 3918 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0108755E-13 -7.0388514E-13 midg,1,midg; midg,igrid,midg -1.5086837E-13 1.6225683E-12 1,midg,midg; igrid,midg,midg 3.9834610E-13 -9.6555001E-13 gauss-seidel spectral radius is 0.9710160 estimated iterations to convergence 49 setup time was (sec) 0.3700000 now iterating at: 14:37:15 rms-change max change #iterations 1.8034967E-02 5.230610 at 10iterations 6.1378005E-04 0.1402645 at 20iterations 4.9987480E-05 1.3027191E-02 at 30iterations 6.5419804E-06 1.7433167E-03 at 40iterations 9.2094757E-07 2.4795532E-04 at 50iterations finished qdiffx linear iterations at : 14:37:18 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 9.2094757E-07 2.4795532E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 14:37:18 3.566u 0.184s 0:04.22 88.6% 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 Mon Oct 10 2011 at 14:37:18 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: ADP 651 has a net charge of -2.0000 !!! WARNING: MG6 652 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.260311 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): -5.681000 48.70600 ymin,ymax (A): 16.10000 100.8410 zmin,zma (A): 14.75900 72.72600 x,y,z range (A): 54.38700 84.74100 57.96700 scale (grids/A): 1.260311 object centre (A): 21.51250 58.47050 43.74250 number of atom coordinates read : 2667 total number of charged atoms : 2518 net assigned charge : -4.599990 assigned positive charge : 412.9636 centred at (gu) : 86.92365 110.3359 87.01316 assigned negative charge : -417.5643 centred at (gu) : 87.11464 110.1814 87.11746 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 32878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26199 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 7010 mr = 20250 m= 317 mr = 3752 m= 5 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 16149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 529 ## 18 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 17246 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) : 0.4201036 object centre at (A) : 21.51250 58.47050 43.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0441392E-04 8.1625022E-04 midg,1,midg; midg,igrid,midg -7.2398707E-03 -9.4239172E-03 1,midg,midg; igrid,midg,midg -5.5150758E-04 -7.1662519E-04 gauss-seidel spectral radius is 0.9967802 estimated iterations to convergence 141 setup time was (sec) 0.4000000 now iterating at: 14:37:19 rms-change max change #iterations 1.714346 188.4660 at 10iterations 0.5335447 43.25832 at 20iterations 0.1649455 12.12478 at 30iterations 5.1654443E-02 3.649472 at 40iterations 1.6103258E-02 0.8839092 at 50iterations 5.0576483E-03 0.2862978 at 60iterations 1.6011806E-03 9.1016710E-02 at 70iterations 5.1290635E-04 2.6802063E-02 at 80iterations 1.7652480E-04 1.1918068E-02 at 90iterations 6.6987915E-05 3.9596558E-03 at 100iterations 2.9423036E-05 1.6632080E-03 at 110iterations 1.4527399E-05 7.7819824E-04 at 120iterations finished qdiffx linear iterations at : 14:37:26 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.4527399E-05 7.7819824E-04 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 14:37:27 7.416u 0.223s 0:08.25 92.4% 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 Mon Oct 10 2011 at 14:37:27 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: ADP 651 has a net charge of -2.0000 !!! WARNING: MG6 652 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.890466 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): -5.681000 48.70600 ymin,ymax (A): 16.10000 100.8410 zmin,zma (A): 14.75900 72.72600 x,y,z range (A): 54.38700 84.74100 57.96700 scale (grids/A): 1.890466 object centre (A): 21.51250 58.47050 43.74250 number of atom coordinates read : 2667 total number of charged atoms : 2518 net assigned charge : -4.599990 assigned positive charge : 412.9636 centred at (gu) : 85.38538 120.5040 85.51957 assigned negative charge : -417.5643 centred at (gu) : 85.67191 120.2721 85.67613 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26199 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 27284 mr = 50835 m= 4472 mr = 18977 m= 274 mr = 2578 m= 5 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 36439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 19811 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) : 1.260311 object centre at (A) : 21.51250 58.47050 43.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8576605E-02 2.6308907E-02 midg,1,midg; midg,igrid,midg -0.1324117 -0.1909091 1,midg,midg; igrid,midg,midg -1.6360270E-02 -1.0653271E-02 gauss-seidel spectral radius is 0.9985529 estimated iterations to convergence 208 setup time was (sec) 0.6600000 now iterating at: 14:37:28 rms-change max change #iterations 5.215647 270.3103 at 10iterations 2.452754 104.8741 at 20iterations 1.146246 54.90084 at 30iterations 0.5337791 19.07526 at 40iterations 0.2479820 8.395683 at 50iterations 0.1141316 3.731567 at 60iterations 5.2608993E-02 1.840754 at 70iterations 2.4301119E-02 0.7555218 at 80iterations 1.1191290E-02 0.3935881 at 90iterations 5.1449472E-03 0.1654077 at 100iterations 2.3786668E-03 7.6915741E-02 at 110iterations 1.0938485E-03 3.4845352E-02 at 120iterations 5.0674035E-04 1.5064716E-02 at 130iterations 2.3872756E-04 8.7270737E-03 at 140iterations 1.1344544E-04 4.1751862E-03 at 150iterations 5.5988632E-05 1.6298294E-03 at 160iterations 2.9242594E-05 9.5558167E-04 at 170iterations 1.6237405E-05 5.1879883E-04 at 180iterations finished qdiffx linear iterations at : 14:37:38 total time elapsed so far: 11.39000 # loops : 180 mean,max change (kT/e) : 1.6237405E-05 5.1879883E-04 energy calculations done at 11.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 14:37:39 11.526u 0.210s 0:12.14 96.6% 0+0k 0+0io 0pf+0w