Tue Oct 11 08:06:18 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 08:06:19 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2404 !!! WARNING: WAT 3 has a net charge of -0.8340 !!! WARNING: WAT 4 has a net charge of -0.8340 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: 0.6147045 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): -16.89100 27.93100 ymin,ymax (A): 13.48600 71.40000 zmin,zma (A): -13.31200 38.42300 x,y,z range (A): 44.82200 57.91400 51.73500 scale (grids/A): 0.6147045 object centre (A): 5.520000 42.44300 12.55550 number of atom coordinates read : 2404 total number of charged atoms : 2259 net assigned charge : 7.332021 assigned positive charge : 351.8389 centred at (gu) : 89.33952 90.01669 90.81926 assigned negative charge : -344.5077 centred at (gu) : 89.28688 90.11926 90.74049 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6149 nv = 96 ne = 84 npr = 47831 no. pairs analyzed = 47831 no. exposed pairs = 3174 no. arc points = 22846 no. surface atoms = 1065 nbur = 1339 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3152 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3700000 number of dielectric boundary points 3310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7492 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6005097E-10 1.0715547E-08 midg,1,midg; midg,igrid,midg 1.0082807E-08 -2.4313238E-10 1,midg,midg; igrid,midg,midg 2.6554678E-09 6.6190236E-09 gauss-seidel spectral radius is 0.9862883 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 08:06:19 rms-change max change #iterations 0.1186238 19.00480 at 10iterations 1.0543060E-02 1.536159 at 20iterations 9.2446955E-04 0.1580896 at 30iterations 8.4314896E-05 1.1830330E-02 at 40iterations 7.5252469E-06 1.2760162E-03 at 50iterations finished qdiffx linear iterations at : 08:06:22 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 7.5252469E-06 1.2760162E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 08:06:23 4.025u 0.167s 0:04.55 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 Tue Oct 11 2011 at 08:06:23 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2404 !!! WARNING: WAT 3 has a net charge of -0.8340 !!! WARNING: WAT 4 has a net charge of -0.8340 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: 1.844114 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): -16.89100 27.93100 ymin,ymax (A): 13.48600 71.40000 zmin,zma (A): -13.31200 38.42300 x,y,z range (A): 44.82200 57.91400 51.73500 scale (grids/A): 1.844114 object centre (A): 5.520000 42.44300 12.55550 number of atom coordinates read : 2404 total number of charged atoms : 2259 net assigned charge : 7.332021 assigned positive charge : 351.8389 centred at (gu) : 88.01804 90.04948 92.45725 assigned negative charge : -344.5077 centred at (gu) : 87.86053 90.35757 92.22125 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22846 grid for indexing accessible points = 1.400000 m= 22374 mr = 44427 m= 3047 mr = 15630 m= 147 mr = 1676 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 472 time to turn everything in is 0.6000000 number of dielectric boundary points 30525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17679 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) : 0.6147045 object centre at (A) : 5.520000 42.44300 12.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2773145E-03 1.8122071E-02 midg,1,midg; midg,igrid,midg 4.1197978E-02 -1.6832544E-02 1,midg,midg; igrid,midg,midg 1.0145219E-02 1.0937780E-02 gauss-seidel spectral radius is 0.9985310 estimated iterations to convergence 207 setup time was (sec) 0.9400000 now iterating at: 08:06:24 rms-change max change #iterations 3.715973 171.0851 at 10iterations 1.683738 66.12163 at 20iterations 0.7691193 26.24584 at 30iterations 0.3482502 14.18740 at 40iterations 0.1582987 5.723641 at 50iterations 7.1738243E-02 2.646784 at 60iterations 3.2671031E-02 1.124885 at 70iterations 1.4811670E-02 0.4928484 at 80iterations 6.7278249E-03 0.2231750 at 90iterations 3.0706387E-03 0.1112251 at 100iterations 1.3900534E-03 4.8126221E-02 at 110iterations 6.3485018E-04 2.1674156E-02 at 120iterations finished qdiffx linear iterations at : 08:06:32 total time elapsed so far: 8.600000 # loops : 120 mean,max change (kT/e) : 6.3485018E-04 2.1674156E-02 energy calculations done at 8.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.840000 DelPhi exited at 08:06:33 8.847u 0.200s 0:09.57 94.4% 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 Tue Oct 11 2011 at 08:06:33 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2404 !!! WARNING: WAT 3 has a net charge of -0.8340 !!! WARNING: WAT 4 has a net charge of -0.8340 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: 2.766171 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): -16.89100 27.93100 ymin,ymax (A): 13.48600 71.40000 zmin,zma (A): -13.31200 38.42300 x,y,z range (A): 44.82200 57.91400 51.73500 scale (grids/A): 2.766171 object centre (A): 5.520000 42.44300 12.55550 number of atom coordinates read : 2404 total number of charged atoms : 2259 net assigned charge : 7.332021 assigned positive charge : 351.8389 centred at (gu) : 87.02680 90.07407 93.68573 assigned negative charge : -344.5077 centred at (gu) : 86.79092 90.53638 93.33189 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 154511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22846 grid for indexing accessible points = 1.400000 m= 73378 mr = 108523 m= 24751 mr = 58264 m= 5136 mr = 18948 m= 668 mr = 3581 m= 22 mr = 412 m= 0 mr = 10 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 1451 time to turn everything in is 1.490000 number of dielectric boundary points 68728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 18069 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) : 1.844114 object centre at (A) : 5.520000 42.44300 12.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7049993E-02 0.2068686 midg,1,midg; midg,igrid,midg 0.6259483 -0.4520031 1,midg,midg; igrid,midg,midg 0.1406446 0.1145335 gauss-seidel spectral radius is 0.9992342 estimated iterations to convergence 285 setup time was (sec) 1.830000 now iterating at: 08:06:35 rms-change max change #iterations 9.123589 327.2905 at 10iterations 5.350301 137.0148 at 20iterations 3.104907 83.44614 at 30iterations 1.788418 41.89622 at 40iterations 1.028245 21.36167 at 50iterations 0.5877899 13.62492 at 60iterations 0.3357614 7.555953 at 70iterations 0.1919169 3.761636 at 80iterations 0.1091924 2.328293 at 90iterations 6.2339175E-02 1.226327 at 100iterations 3.5453357E-02 0.7194099 at 110iterations 2.0158252E-02 0.4170399 at 120iterations 1.1484768E-02 0.2395744 at 130iterations 6.5360842E-03 0.1338577 at 140iterations 3.7248353E-03 7.6171875E-02 at 150iterations 2.1141155E-03 4.2009354E-02 at 160iterations 1.2027451E-03 2.5235176E-02 at 170iterations 6.8349042E-04 1.2671471E-02 at 180iterations finished qdiffx linear iterations at : 08:06:47 total time elapsed so far: 14.10000 # loops : 180 mean,max change (kT/e) : 6.8349042E-04 1.2671471E-02 energy calculations done at 14.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.34000 DelPhi exited at 08:06:48 14.344u 0.245s 0:15.06 96.8% 0+0k 0+0io 0pf+0w