Sat Oct 8 17:25:00 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 Sat Oct 8 2011 at 17:25:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3742 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: 0.5439516 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): -1.662000 60.34600 ymin,ymax (A): -18.56100 44.44000 zmin,zma (A): -6.473000 58.97400 x,y,z range (A): 62.00800 63.00100 65.44701 scale (grids/A): 0.5439516 object centre (A): 29.34200 12.93950 26.25050 number of atom coordinates read : 3742 total number of charged atoms : 3592 net assigned charge : -8.999969 assigned positive charge : 563.8444 centred at (gu) : 88.76166 86.77346 90.77274 assigned negative charge : -572.8467 centred at (gu) : 88.82490 86.77598 90.79792 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7180 nv = 96 ne = 84 npr = 75114 no. pairs analyzed = 75114 no. exposed pairs = 4880 no. arc points = 34823 no. surface atoms = 1629 nbur = 2113 mkacc time = 0.2100000 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 = 1.568000 m= 301 mr = 3629 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3500 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6650587E-10 -8.6081192E-10 midg,1,midg; midg,igrid,midg -1.0925676E-09 -2.4892410E-10 1,midg,midg; igrid,midg,midg -2.4523264E-11 -7.4771989E-10 gauss-seidel spectral radius is 0.9826374 estimated iterations to convergence 63 setup time was (sec) 0.7600000 now iterating at: 17:25:01 rms-change max change #iterations 8.0069251E-02 13.81868 at 10iterations 5.5117854E-03 0.8237553 at 20iterations 5.5062154E-04 9.7354889E-02 at 30iterations 1.2248983E-04 2.3101807E-02 at 40iterations 3.5395544E-05 6.4754486E-03 at 50iterations finished qdiffx linear iterations at : 17:25:05 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 3.5395544E-05 6.4754486E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 17:25:05 4.474u 0.254s 0:05.00 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 Sat Oct 8 2011 at 17:25:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3742 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: 1.631855 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): -1.662000 60.34600 ymin,ymax (A): -18.56100 44.44000 zmin,zma (A): -6.473000 58.97400 x,y,z range (A): 62.00800 63.00100 65.44701 scale (grids/A): 1.631855 object centre (A): 29.34200 12.93950 26.25050 number of atom coordinates read : 3742 total number of charged atoms : 3592 net assigned charge : -8.999969 assigned positive charge : 563.8444 centred at (gu) : 86.28397 80.31935 92.31730 assigned negative charge : -572.8467 centred at (gu) : 86.47439 80.32788 92.39333 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24593 mr = 53622 m= 2576 mr = 16409 m= 66 mr = 1181 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 35768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 383 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 27500 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) : 0.5439516 object centre at (A) : 29.34200 12.93950 26.25050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2036962E-04 -1.0301560E-02 midg,1,midg; midg,igrid,midg -2.6557440E-02 -6.0784658E-03 1,midg,midg; igrid,midg,midg -1.0357275E-02 -2.6685024E-02 gauss-seidel spectral radius is 0.9982559 estimated iterations to convergence 190 setup time was (sec) 0.9200000 now iterating at: 17:25:07 rms-change max change #iterations 3.798309 173.9924 at 10iterations 1.607781 57.76460 at 20iterations 0.6797378 22.81692 at 30iterations 0.2876874 9.502184 at 40iterations 0.1225044 4.137827 at 50iterations 5.1913936E-02 1.665191 at 60iterations 2.2092519E-02 0.7822404 at 70iterations 9.3911542E-03 0.3327875 at 80iterations 3.9980020E-03 0.1337757 at 90iterations 1.7132458E-03 5.7586670E-02 at 100iterations 7.4042083E-04 2.6306152E-02 at 110iterations 3.2701038E-04 1.0888100E-02 at 120iterations finished qdiffx linear iterations at : 17:25:15 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 3.2701038E-04 1.0888100E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 17:25:16 9.547u 0.268s 0:10.08 97.2% 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 Sat Oct 8 2011 at 17:25:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3742 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: 2.447782 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): -1.662000 60.34600 ymin,ymax (A): -18.56100 44.44000 zmin,zma (A): -6.473000 58.97400 x,y,z range (A): 62.00800 63.00100 65.44701 scale (grids/A): 2.447782 object centre (A): 29.34200 12.93950 26.25050 number of atom coordinates read : 3742 total number of charged atoms : 3592 net assigned charge : -8.999969 assigned positive charge : 563.8444 centred at (gu) : 84.42567 75.47871 93.47576 assigned negative charge : -572.8467 centred at (gu) : 84.71130 75.49176 93.58976 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 184982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85412 mr = 131405 m= 24197 mr = 66552 m= 3921 mr = 17727 m= 240 mr = 2369 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 80638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 28698 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) : 1.631855 object centre at (A) : 29.34200 12.93950 26.25050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2744583E-02 5.8170982E-02 midg,1,midg; midg,igrid,midg -0.4090363 -9.1470078E-02 1,midg,midg; igrid,midg,midg -0.1706103 -0.5241841 gauss-seidel spectral radius is 0.9991756 estimated iterations to convergence 275 setup time was (sec) 1.890000 now iterating at: 17:25:18 rms-change max change #iterations 9.835436 253.9538 at 10iterations 5.629811 137.0778 at 20iterations 3.202524 77.53774 at 30iterations 1.809372 39.49984 at 40iterations 1.018925 23.35632 at 50iterations 0.5717474 12.54043 at 60iterations 0.3207586 6.736499 at 70iterations 0.1798011 3.938201 at 80iterations 0.1005054 2.366768 at 90iterations 5.6157384E-02 1.376057 at 100iterations 3.1383015E-02 0.6243458 at 110iterations 1.7513724E-02 0.3350515 at 120iterations 9.7886762E-03 0.2013483 at 130iterations 5.4835631E-03 0.1014290 at 140iterations 3.0703123E-03 6.1268806E-02 at 150iterations 1.7271104E-03 3.3549309E-02 at 160iterations 9.7949489E-04 1.9011974E-02 at 170iterations 5.6289538E-04 1.1126518E-02 at 180iterations finished qdiffx linear iterations at : 17:25:31 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 5.6289538E-04 1.1126518E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 17:25:32 15.540u 0.296s 0:16.12 98.2% 0+0k 0+0io 0pf+0w