Sat Oct 15 14:56:52 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 15 2011 at 14:56:52 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2329 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: 0.6335985 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): 11.25400 57.98500 ymin,ymax (A): 1.045000 57.23200 zmin,zma (A): 6.545000 60.38500 x,y,z range (A): 46.73100 56.18700 53.84000 scale (grids/A): 0.6335985 object centre (A): 34.61950 29.13850 33.46500 number of atom coordinates read : 2329 total number of charged atoms : 2194 net assigned charge : -1.999994 assigned positive charge : 339.9644 centred at (gu) : 90.31229 91.04758 89.76405 assigned negative charge : -341.9651 centred at (gu) : 90.32153 91.02630 89.79738 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6256 nv = 96 ne = 84 npr = 47905 no. pairs analyzed = 47905 no. exposed pairs = 3070 no. arc points = 21457 no. surface atoms = 1029 nbur = 1300 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3307 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2089 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4730197E-10 -5.0606932E-09 midg,1,midg; midg,igrid,midg -3.4259930E-09 -7.3698980E-10 1,midg,midg; igrid,midg,midg -1.5458953E-09 -3.4611722E-09 gauss-seidel spectral radius is 0.9870747 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 14:56:53 rms-change max change #iterations 0.1309202 21.92693 at 10iterations 1.2482963E-02 1.903671 at 20iterations 1.2400993E-03 0.2025528 at 30iterations 1.1976218E-04 1.7160416E-02 at 40iterations 1.4284763E-05 2.2125244E-03 at 50iterations finished qdiffx linear iterations at : 14:56:56 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4284763E-05 2.2125244E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:56:56 3.372u 0.174s 0:03.87 91.4% 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 15 2011 at 14:56:56 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2329 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: 1.900796 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): 11.25400 57.98500 ymin,ymax (A): 1.045000 57.23200 zmin,zma (A): 6.545000 60.38500 x,y,z range (A): 46.73100 56.18700 53.84000 scale (grids/A): 1.900796 object centre (A): 34.61950 29.13850 33.46500 number of atom coordinates read : 2329 total number of charged atoms : 2194 net assigned charge : -1.999994 assigned positive charge : 339.9644 centred at (gu) : 90.93665 93.14255 89.29176 assigned negative charge : -341.9651 centred at (gu) : 90.96479 93.07899 89.39209 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21457 grid for indexing accessible points = 1.400000 m= 23606 mr = 46135 m= 3676 mr = 16696 m= 212 mr = 2135 m= 3 mr = 67 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 0.5300000 number of dielectric boundary points 30121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17250 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) : 0.6335985 object centre at (A) : 34.61950 29.13850 33.46500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9363208E-02 9.1977753E-03 midg,1,midg; midg,igrid,midg -4.6983991E-02 -2.3499729E-02 1,midg,midg; igrid,midg,midg -4.9465513E-03 8.9143170E-03 gauss-seidel spectral radius is 0.9986050 estimated iterations to convergence 212 setup time was (sec) 0.8200000 now iterating at: 14:56:57 rms-change max change #iterations 3.909992 167.6650 at 10iterations 1.806603 68.20558 at 20iterations 0.8351411 30.86073 at 30iterations 0.3866650 12.97858 at 40iterations 0.1801572 6.725343 at 50iterations 8.3418123E-02 2.760281 at 60iterations 3.8861986E-02 1.436974 at 70iterations 1.7937265E-02 0.5804100 at 80iterations 8.3580445E-03 0.2891159 at 90iterations 3.8805676E-03 0.1353483 at 100iterations 1.8022603E-03 5.6392670E-02 at 110iterations 8.3998905E-04 3.0486584E-02 at 120iterations finished qdiffx linear iterations at : 14:57:04 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 8.3998905E-04 3.0486584E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 14:57:04 7.510u 0.173s 0:08.06 95.2% 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 15 2011 at 14:57:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2329 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.851193 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): 11.25400 57.98500 ymin,ymax (A): 1.045000 57.23200 zmin,zma (A): 6.545000 60.38500 x,y,z range (A): 46.73100 56.18700 53.84000 scale (grids/A): 2.851193 object centre (A): 34.61950 29.13850 33.46500 number of atom coordinates read : 2329 total number of charged atoms : 2194 net assigned charge : -1.999994 assigned positive charge : 339.9644 centred at (gu) : 91.40499 94.71375 88.93764 assigned negative charge : -341.9651 centred at (gu) : 91.44720 94.61842 89.08814 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 156542 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21457 grid for indexing accessible points = 1.400000 m= 76119 mr = 112245 m= 27607 mr = 60813 m= 6558 mr = 21540 m= 901 mr = 4702 m= 62 mr = 554 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 67916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 17552 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) : 1.900796 object centre at (A) : 34.61950 29.13850 33.46500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4685173 0.1082361 midg,1,midg; midg,igrid,midg -0.9733226 -0.1748339 1,midg,midg; igrid,midg,midg -3.7176728E-02 0.1312595 gauss-seidel spectral radius is 0.9992495 estimated iterations to convergence 288 setup time was (sec) 1.610000 now iterating at: 14:57:06 rms-change max change #iterations 9.357745 400.7945 at 10iterations 5.459302 190.2036 at 20iterations 3.165847 86.48200 at 30iterations 1.835681 44.40594 at 40iterations 1.060579 20.73072 at 50iterations 0.6105623 12.63089 at 60iterations 0.3509211 7.333801 at 70iterations 0.2019214 3.742551 at 80iterations 0.1161373 2.298203 at 90iterations 6.6664718E-02 1.250820 at 100iterations 3.8104009E-02 0.7253070 at 110iterations 2.1867694E-02 0.4622030 at 120iterations 1.2559439E-02 0.2488327 at 130iterations 7.1857069E-03 0.1447983 at 140iterations 4.1290172E-03 7.7526093E-02 at 150iterations 2.3720143E-03 4.6789169E-02 at 160iterations 1.3678555E-03 2.6582718E-02 at 170iterations 7.9505821E-04 1.6277313E-02 at 180iterations finished qdiffx linear iterations at : 14:57:17 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 7.9505821E-04 1.6277313E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 14:57:17 12.526u 0.205s 0:13.07 97.3% 0+0k 0+0io 0pf+0w