Sun Oct 9 03:33:47 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 Sun Oct 9 2011 at 03:33:48 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4472 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.4223865 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): -53.51500 3.146000 ymin,ymax (A): -83.04000 -18.00100 zmin,zma (A): -28.01300 56.27000 x,y,z range (A): 56.66100 65.03900 84.28300 scale (grids/A): 0.4223865 object centre (A): -25.18450 -50.52050 14.12850 number of atom coordinates read : 4472 total number of charged atoms : 4239 net assigned charge : 19.99999 assigned positive charge : 657.4973 centred at (gu) : 89.87732 88.23960 86.07997 assigned negative charge : -637.5019 centred at (gu) : 89.87979 88.27324 86.01183 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4694 nv = 96 ne = 84 npr = 90340 no. pairs analyzed = 90340 no. exposed pairs = 5746 no. arc points = 40250 no. surface atoms = 1940 nbur = 2532 mkacc time = 0.1700000 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 = 1.988000 m= 113 mr = 2119 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3187 ## 694 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6461 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6195383E-12 1.2272747E-12 midg,1,midg; midg,igrid,midg 5.6380382E-12 9.8540772E-13 1,midg,midg; igrid,midg,midg 2.6175769E-12 2.3156553E-12 gauss-seidel spectral radius is 0.9714338 estimated iterations to convergence 49 setup time was (sec) 0.5000000 now iterating at: 03:33:48 rms-change max change #iterations 2.6216187E-02 10.66611 at 10iterations 2.8102885E-03 0.5417824 at 20iterations 7.8600453E-04 0.1608791 at 30iterations 2.3134031E-04 4.7582626E-02 at 40iterations 6.8280868E-05 1.4055252E-02 at 50iterations finished qdiffx linear iterations at : 03:33:52 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 6.8280868E-05 1.4055252E-02 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 03:33:52 3.700u 0.547s 0:04.68 90.5% 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 Sun Oct 9 2011 at 03:33:52 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4472 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.267159 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): -53.51500 3.146000 ymin,ymax (A): -83.04000 -18.00100 zmin,zma (A): -28.01300 56.27000 x,y,z range (A): 56.66100 65.03900 84.28300 scale (grids/A): 1.267159 object centre (A): -25.18450 -50.52050 14.12850 number of atom coordinates read : 4472 total number of charged atoms : 4239 net assigned charge : 19.99999 assigned positive charge : 657.4973 centred at (gu) : 89.63020 84.71698 78.23843 assigned negative charge : -637.5019 centred at (gu) : 89.63900 84.81937 78.03497 start vw surface at 0.1300000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 55169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40250 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 12291 mr = 35573 m= 594 mr = 7137 m= 4 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 507 time to turn everything in is 0.3200000 number of dielectric boundary points 25227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 725 ## 25 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 29137 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) : 0.4223865 object centre at (A) : -25.18450 -50.52050 14.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2150628E-02 3.4892831E-03 midg,1,midg; midg,igrid,midg 4.5834221E-03 1.7946229E-03 1,midg,midg; igrid,midg,midg 9.6392503E-04 7.6586241E-04 gauss-seidel spectral radius is 0.9970529 estimated iterations to convergence 147 setup time was (sec) 0.5200000 now iterating at: 03:33:53 rms-change max change #iterations 2.211208 124.6872 at 10iterations 0.7315993 32.77773 at 20iterations 0.2402668 9.986610 at 30iterations 7.9831891E-02 3.546015 at 40iterations 2.6862353E-02 1.263708 at 50iterations 9.4322031E-03 0.4214058 at 60iterations 3.7912990E-03 0.1845856 at 70iterations 1.9078414E-03 0.1033707 at 80iterations 1.1455789E-03 5.3871155E-02 at 90iterations 7.4424606E-04 3.4223557E-02 at 100iterations 4.9261964E-04 2.2609711E-02 at 110iterations 3.2806251E-04 1.5039444E-02 at 120iterations finished qdiffx linear iterations at : 03:34:00 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 3.2806251E-04 1.5039444E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 03:34:01 7.619u 0.242s 0:08.28 94.8% 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 Sun Oct 9 2011 at 03:34:01 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4472 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.900739 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): -53.51500 3.146000 ymin,ymax (A): -83.04000 -18.00100 zmin,zma (A): -28.01300 56.27000 x,y,z range (A): 56.66100 65.03900 84.28300 scale (grids/A): 1.900739 object centre (A): -25.18450 -50.52050 14.12850 number of atom coordinates read : 4472 total number of charged atoms : 4239 net assigned charge : 19.99999 assigned positive charge : 657.4973 centred at (gu) : 89.44492 82.07518 72.35735 assigned negative charge : -637.5019 centred at (gu) : 89.45834 82.22911 72.05231 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 129655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40250 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 48266 mr = 89325 m= 8171 mr = 35128 m= 546 mr = 4994 m= 11 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1644 time to turn everything in is 0.7300000 number of dielectric boundary points 57037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 33327 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) : 1.267159 object centre at (A) : -25.18450 -50.52050 14.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2766645 5.4359157E-02 midg,1,midg; midg,igrid,midg 0.1161588 4.6910118E-02 1,midg,midg; igrid,midg,midg 2.6050124E-02 1.7408725E-02 gauss-seidel spectral radius is 0.9987764 estimated iterations to convergence 226 setup time was (sec) 0.9900000 now iterating at: 03:34:02 rms-change max change #iterations 6.817016 217.2549 at 10iterations 3.448207 107.5718 at 20iterations 1.735090 51.25709 at 30iterations 0.8637144 22.28382 at 40iterations 0.4299412 11.11541 at 50iterations 0.2125978 5.356627 at 60iterations 0.1049908 3.089916 at 70iterations 5.1816452E-02 1.322990 at 80iterations 2.5530837E-02 0.6531029 at 90iterations 1.2596861E-02 0.3013020 at 100iterations 6.2385243E-03 0.1696148 at 110iterations 3.1141797E-03 7.8927994E-02 at 120iterations 1.5808151E-03 3.9842606E-02 at 130iterations 8.3913404E-04 2.1728516E-02 at 140iterations 4.7465120E-04 1.3593674E-02 at 150iterations 2.9410725E-04 8.7604523E-03 at 160iterations 1.9678248E-04 5.3119659E-03 at 170iterations 1.4010730E-04 3.7765503E-03 at 180iterations finished qdiffx linear iterations at : 03:34:13 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 1.4010730E-04 3.7765503E-03 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 03:34:13 12.195u 0.230s 0:12.84 96.7% 0+0k 0+0io 0pf+0w