Tue Oct 11 03:15:30 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 03:15:30 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3432 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 295 has a net charge of 0.5140 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: 0.5386919 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): 4.450000 70.53600 ymin,ymax (A): 32.08700 94.04300 zmin,zma (A): 25.06000 79.39500 x,y,z range (A): 66.08601 61.95600 54.33501 scale (grids/A): 0.5386919 object centre (A): 37.49300 63.06500 52.22750 number of atom coordinates read : 3432 total number of charged atoms : 3285 net assigned charge : -7.910981 assigned positive charge : 517.6763 centred at (gu) : 87.76643 91.67071 88.30460 assigned negative charge : -525.5887 centred at (gu) : 87.71585 91.65857 88.32829 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6426 nv = 96 ne = 84 npr = 69496 no. pairs analyzed = 69496 no. exposed pairs = 4434 no. arc points = 30723 no. surface atoms = 1491 nbur = 1941 mkacc time = 0.1200000 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 = 1.596000 m= 249 mr = 3284 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3194 ## 466 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3170616E-10 -3.3070990E-10 midg,1,midg; midg,igrid,midg -2.8795175E-10 -4.3354928E-10 1,midg,midg; igrid,midg,midg -1.1573302E-09 -4.2505686E-11 gauss-seidel spectral radius is 0.9822713 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 03:15:31 rms-change max change #iterations 7.3983341E-02 11.69372 at 10iterations 5.1399856E-03 0.7332878 at 20iterations 5.1504764E-04 6.8196535E-02 at 30iterations 1.0325224E-04 1.4359877E-02 at 40iterations 2.5747122E-05 3.7217140E-03 at 50iterations finished qdiffx linear iterations at : 03:15:33 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.5747122E-05 3.7217140E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:15:34 3.473u 0.166s 0:04.11 88.3% 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 Tue Oct 11 2011 at 03:15:34 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3432 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 295 has a net charge of 0.5140 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: 1.616076 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): 4.450000 70.53600 ymin,ymax (A): 32.08700 94.04300 zmin,zma (A): 25.06000 79.39500 x,y,z range (A): 66.08601 61.95600 54.33501 scale (grids/A): 1.616076 object centre (A): 37.49300 63.06500 52.22750 number of atom coordinates read : 3432 total number of charged atoms : 3285 net assigned charge : -7.910981 assigned positive charge : 517.6763 centred at (gu) : 83.29852 95.01100 84.91328 assigned negative charge : -525.5887 centred at (gu) : 83.14723 94.97535 84.98441 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21623 mr = 47078 m= 2208 mr = 14727 m= 60 mr = 1092 m= 0 mr = 5 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 0.3700000 number of dielectric boundary points 31547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 424 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 25100 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) : 0.5386919 object centre at (A) : 37.49300 63.06500 52.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9090541E-03 -2.8447818E-03 midg,1,midg; midg,igrid,midg -3.7310142E-03 4.0713749E-03 1,midg,midg; igrid,midg,midg -2.0426122E-02 2.7866526E-02 gauss-seidel spectral radius is 0.9981847 estimated iterations to convergence 186 setup time was (sec) 0.5900000 now iterating at: 03:15:35 rms-change max change #iterations 3.519226 175.3747 at 10iterations 1.460640 69.26238 at 20iterations 0.6085857 23.83428 at 30iterations 0.2535143 11.84555 at 40iterations 0.1056986 3.891134 at 50iterations 4.4116206E-02 1.480933 at 60iterations 1.8441435E-02 0.6098194 at 70iterations 7.7184746E-03 0.2732811 at 80iterations 3.2746093E-03 0.1128387 at 90iterations 1.3963919E-03 5.0529480E-02 at 100iterations 6.1356596E-04 2.1425247E-02 at 110iterations 2.8291062E-04 1.1287212E-02 at 120iterations finished qdiffx linear iterations at : 03:15:42 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.8291062E-04 1.1287212E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:15:42 7.796u 0.198s 0:08.29 96.2% 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 03:15:42 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3432 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 295 has a net charge of 0.5140 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: 2.424114 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): 4.450000 70.53600 ymin,ymax (A): 32.08700 94.04300 zmin,zma (A): 25.06000 79.39500 x,y,z range (A): 66.08601 61.95600 54.33501 scale (grids/A): 2.424114 object centre (A): 37.49300 63.06500 52.22750 number of atom coordinates read : 3432 total number of charged atoms : 3285 net assigned charge : -7.910981 assigned positive charge : 517.6763 centred at (gu) : 79.94734 97.51632 82.36967 assigned negative charge : -525.5887 centred at (gu) : 79.72066 97.46293 82.47643 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 75570 mr = 115606 m= 21129 mr = 59138 m= 3427 mr = 15780 m= 195 mr = 2283 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 2153 time to turn everything in is 0.8800000 number of dielectric boundary points 71199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 26245 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) : 1.616076 object centre at (A) : 37.49300 63.06500 52.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1214885 -5.5817526E-02 midg,1,midg; midg,igrid,midg 1.9556530E-02 0.1070842 1,midg,midg; igrid,midg,midg -0.4882224 0.5941663 gauss-seidel spectral radius is 0.9991471 estimated iterations to convergence 270 setup time was (sec) 1.120000 now iterating at: 03:15:44 rms-change max change #iterations 9.308460 330.9152 at 10iterations 5.274107 128.5027 at 20iterations 2.964856 70.83356 at 30iterations 1.661917 41.46799 at 40iterations 0.9268175 26.44785 at 50iterations 0.5160201 11.49755 at 60iterations 0.2865562 6.072239 at 70iterations 0.1592867 3.843359 at 80iterations 8.8119745E-02 1.871701 at 90iterations 4.8816826E-02 1.069049 at 100iterations 2.7125617E-02 0.5902824 at 110iterations 1.4948032E-02 0.3728867 at 120iterations 8.2488004E-03 0.1894903 at 130iterations 4.5753862E-03 0.1056938 at 140iterations 2.5293019E-03 5.1736832E-02 at 150iterations 1.4050279E-03 3.0544281E-02 at 160iterations 7.8227912E-04 1.5688896E-02 at 170iterations 4.3891219E-04 8.5536242E-03 at 180iterations finished qdiffx linear iterations at : 03:15:55 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 4.3891219E-04 8.5536242E-03 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 03:15:55 12.457u 0.227s 0:13.06 97.0% 0+0k 0+0io 0pf+0w