Tue Oct 11 03:15:31 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 03:15:31 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5335091 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): -38.47200 21.33000 ymin,ymax (A): -7.707000 46.39600 zmin,zma (A): -70.59200 -3.864000 x,y,z range (A): 59.80200 54.10300 66.72800 scale (grids/A): 0.5335091 object centre (A): -8.571000 19.34450 -37.22800 number of atom coordinates read : 3525 total number of charged atoms : 3378 net assigned charge : -8.068971 assigned positive charge : 537.7950 centred at (gu) : 92.10680 91.13110 92.33957 assigned negative charge : -545.8658 centred at (gu) : 92.09682 91.10435 92.34856 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6446 nv = 96 ne = 84 npr = 71065 no. pairs analyzed = 71065 no. exposed pairs = 4572 no. arc points = 32049 no. surface atoms = 1519 nbur = 2006 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 = 1.624000 m= 254 mr = 3251 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3289 ## 453 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4679037E-10 -6.2371586E-10 midg,1,midg; midg,igrid,midg -3.2971742E-10 -2.2152503E-10 1,midg,midg; igrid,midg,midg -2.1058191E-10 -4.2415843E-10 gauss-seidel spectral radius is 0.9819361 estimated iterations to convergence 61 setup time was (sec) 0.6000000 now iterating at: 03:15:32 rms-change max change #iterations 7.5945459E-02 12.88354 at 10iterations 4.9845297E-03 0.7959034 at 20iterations 6.1582070E-04 8.2809448E-02 at 30iterations 1.6016488E-04 2.1816254E-02 at 40iterations 4.7850070E-05 6.5240860E-03 at 50iterations finished qdiffx linear iterations at : 03:15:34 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 4.7850070E-05 6.5240860E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:15:35 3.335u 0.191s 0:03.89 90.4% 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 03:15:35 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 227 has a net charge of -0.4750 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: 1.600527 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): -38.47200 21.33000 ymin,ymax (A): -7.707000 46.39600 zmin,zma (A): -70.59200 -3.864000 x,y,z range (A): 59.80200 54.10300 66.72800 scale (grids/A): 1.600527 object centre (A): -8.571000 19.34450 -37.22800 number of atom coordinates read : 3525 total number of charged atoms : 3378 net assigned charge : -8.068971 assigned positive charge : 537.7950 centred at (gu) : 96.31951 93.39247 97.01781 assigned negative charge : -545.8658 centred at (gu) : 96.29012 93.31281 97.04525 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32049 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21866 mr = 48249 m= 2046 mr = 14473 m= 54 mr = 909 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 31939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 25701 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) : 0.5335091 object centre at (A) : -8.571000 19.34450 -37.22800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4590053E-02 -1.7465372E-02 midg,1,midg; midg,igrid,midg -2.6633963E-03 -3.1018001E-03 1,midg,midg; igrid,midg,midg -3.5778019E-03 -2.5587892E-03 gauss-seidel spectral radius is 0.9981566 estimated iterations to convergence 185 setup time was (sec) 0.7900000 now iterating at: 03:15:36 rms-change max change #iterations 3.535888 165.3205 at 10iterations 1.458422 57.73844 at 20iterations 0.6053064 22.38070 at 30iterations 0.2495824 8.570899 at 40iterations 0.1034461 4.424232 at 50iterations 4.2894483E-02 1.466988 at 60iterations 1.7773738E-02 0.6162314 at 70iterations 7.4618091E-03 0.2683144 at 80iterations 3.1779062E-03 0.1154165 at 90iterations 1.3848664E-03 4.7752380E-02 at 100iterations 6.4272422E-04 2.1654129E-02 at 110iterations 3.2824703E-04 1.1365891E-02 at 120iterations finished qdiffx linear iterations at : 03:15:42 total time elapsed so far: 7.090000 # loops : 120 mean,max change (kT/e) : 3.2824703E-04 1.1365891E-02 energy calculations done at 7.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 03:15:43 7.264u 0.217s 0:07.78 96.0% 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 Tue Oct 11 2011 at 03:15:43 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.400791 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): -38.47200 21.33000 ymin,ymax (A): -7.707000 46.39600 zmin,zma (A): -70.59200 -3.864000 x,y,z range (A): 59.80200 54.10300 66.72800 scale (grids/A): 2.400791 object centre (A): -8.571000 19.34450 -37.22800 number of atom coordinates read : 3525 total number of charged atoms : 3378 net assigned charge : -8.068971 assigned positive charge : 537.7950 centred at (gu) : 99.47897 95.08842 100.5263 assigned negative charge : -545.8658 centred at (gu) : 99.43509 94.96896 100.5677 start vw surface at 0.2500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 166866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32049 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76207 mr = 118722 m= 20699 mr = 59119 m= 3063 mr = 15105 m= 172 mr = 1873 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 72151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 26983 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) : 1.600527 object centre at (A) : -8.571000 19.34450 -37.22800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5238003 -0.3861784 midg,1,midg; midg,igrid,midg -4.4913236E-02 -3.4146223E-02 1,midg,midg; igrid,midg,midg -4.1178903E-03 1.9708190E-02 gauss-seidel spectral radius is 0.9991403 estimated iterations to convergence 269 setup time was (sec) 1.670000 now iterating at: 03:15:45 rms-change max change #iterations 9.391006 303.5920 at 10iterations 5.314778 135.3184 at 20iterations 2.986774 82.74368 at 30iterations 1.666896 40.64334 at 40iterations 0.9275548 24.49424 at 50iterations 0.5154575 14.43027 at 60iterations 0.2854918 6.149672 at 70iterations 0.1578995 3.541074 at 80iterations 8.7496676E-02 1.991230 at 90iterations 4.8348155E-02 1.130363 at 100iterations 2.6680313E-02 0.5772054 at 110iterations 1.4732421E-02 0.3352280 at 120iterations 8.1462795E-03 0.1861625 at 130iterations 4.5189871E-03 9.6167564E-02 at 140iterations 2.5146836E-03 5.1925659E-02 at 150iterations 1.4132983E-03 3.0279160E-02 at 160iterations 8.0821052E-04 1.7936707E-02 at 170iterations 4.7339921E-04 1.0819435E-02 at 180iterations finished qdiffx linear iterations at : 03:15:54 total time elapsed so far: 11.18000 # loops : 180 mean,max change (kT/e) : 4.7339921E-04 1.0819435E-02 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 03:15:55 11.357u 0.222s 0:11.98 96.5% 0+0k 0+0io 0pf+0w