Tue Oct 11 08:21:28 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 08:21:28 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2745 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5690082 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): -28.79400 24.19300 ymin,ymax (A): -18.32100 36.80000 zmin,zma (A): -18.54700 44.01800 x,y,z range (A): 52.98700 55.12100 62.56500 scale (grids/A): 0.5690082 object centre (A): -2.300501 9.239499 12.73550 number of atom coordinates read : 2745 total number of charged atoms : 2596 net assigned charge : 7.539025 assigned positive charge : 423.6757 centred at (gu) : 92.13816 90.42602 91.68629 assigned negative charge : -416.1376 centred at (gu) : 92.23560 90.40968 91.61126 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5722 nv = 96 ne = 84 npr = 55211 no. pairs analyzed = 55211 no. exposed pairs = 3519 no. arc points = 25370 no. surface atoms = 1171 nbur = 1574 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 = 1.512000 m= 235 mr = 2878 m= 0 mr = 12 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3900000 number of dielectric boundary points 3067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9632846E-11 3.2401724E-09 midg,1,midg; midg,igrid,midg 8.0613649E-10 1.4893183E-09 1,midg,midg; igrid,midg,midg 1.4999328E-09 -5.0460680E-10 gauss-seidel spectral radius is 0.9840435 estimated iterations to convergence 65 setup time was (sec) 0.6800000 now iterating at: 08:21:29 rms-change max change #iterations 8.7357141E-02 15.81478 at 10iterations 6.4340197E-03 1.067989 at 20iterations 4.9753702E-04 7.6847076E-02 at 30iterations 4.7877158E-05 9.1137886E-03 at 40iterations 7.4946051E-06 1.1730194E-03 at 50iterations finished qdiffx linear iterations at : 08:21:32 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 7.4946051E-06 1.1730194E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 08:21:33 4.370u 0.308s 0:05.00 93.4% 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 08:21:33 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2745 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.707025 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): -28.79400 24.19300 ymin,ymax (A): -18.32100 36.80000 zmin,zma (A): -18.54700 44.01800 x,y,z range (A): 52.98700 55.12100 62.56500 scale (grids/A): 1.707025 object centre (A): -2.300501 9.239499 12.73550 number of atom coordinates read : 2745 total number of charged atoms : 2596 net assigned charge : 7.539025 assigned positive charge : 423.6757 centred at (gu) : 96.41398 91.27764 95.05831 assigned negative charge : -416.1376 centred at (gu) : 96.70673 91.22882 94.83378 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 62183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25370 grid for indexing accessible points = 1.400000 m= 19757 mr = 41230 m= 2318 mr = 13502 m= 76 mr = 1217 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 548 time to turn everything in is 0.6100000 number of dielectric boundary points 28384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20051 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) : 0.5690082 object centre at (A) : -2.300501 9.239499 12.73550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3668128E-03 1.8176349E-02 midg,1,midg; midg,igrid,midg -2.5418235E-03 6.5547475E-03 1,midg,midg; igrid,midg,midg 4.3532616E-03 4.7464324E-03 gauss-seidel spectral radius is 0.9983162 estimated iterations to convergence 193 setup time was (sec) 1.000000 now iterating at: 08:21:34 rms-change max change #iterations 3.537628 224.2454 at 10iterations 1.519073 78.19856 at 20iterations 0.6570233 24.44601 at 30iterations 0.2816735 10.80054 at 40iterations 0.1212713 4.953682 at 50iterations 5.2210674E-02 1.835550 at 60iterations 2.2595784E-02 0.8629379 at 70iterations 9.6935211E-03 0.3869667 at 80iterations 4.1894550E-03 0.1493683 at 90iterations 1.8141507E-03 7.1304321E-02 at 100iterations 7.8102248E-04 3.0487061E-02 at 110iterations 3.4062497E-04 1.2589455E-02 at 120iterations finished qdiffx linear iterations at : 08:21:44 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 3.4062497E-04 1.2589455E-02 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 08:21:44 10.788u 0.357s 0:11.46 97.1% 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 08:21:44 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2745 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.560537 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): -28.79400 24.19300 ymin,ymax (A): -18.32100 36.80000 zmin,zma (A): -18.54700 44.01800 x,y,z range (A): 52.98700 55.12100 62.56500 scale (grids/A): 2.560537 object centre (A): -2.300501 9.239499 12.73550 number of atom coordinates read : 2745 total number of charged atoms : 2596 net assigned charge : 7.539025 assigned positive charge : 423.6757 centred at (gu) : 99.62069 91.91634 97.58731 assigned negative charge : -416.1376 centred at (gu) : 100.0599 91.84319 97.25065 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 144539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25370 grid for indexing accessible points = 1.400000 m= 66762 mr = 101222 m= 20219 mr = 52469 m= 3707 mr = 15099 m= 306 mr = 2516 m= 6 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 1773 time to turn everything in is 1.460000 number of dielectric boundary points 64090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 20754 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) : 1.707025 object centre at (A) : -2.300501 9.239499 12.73550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1003654 0.1804458 midg,1,midg; midg,igrid,midg -5.7308692E-02 -4.1411791E-02 1,midg,midg; igrid,midg,midg 1.2897435E-02 7.6787882E-02 gauss-seidel spectral radius is 0.9991749 estimated iterations to convergence 275 setup time was (sec) 1.880000 now iterating at: 08:21:46 rms-change max change #iterations 8.868348 306.2710 at 10iterations 5.012492 128.9678 at 20iterations 2.816270 63.73946 at 30iterations 1.580933 39.10316 at 40iterations 0.8841512 20.20472 at 50iterations 0.4940414 10.33607 at 60iterations 0.2766759 6.930421 at 70iterations 0.1545991 3.348236 at 80iterations 8.6265393E-02 1.902666 at 90iterations 4.8050631E-02 1.009495 at 100iterations 2.6813433E-02 0.5626884 at 110iterations 1.4915431E-02 0.3152399 at 120iterations 8.3228461E-03 0.1788826 at 130iterations 4.6223458E-03 9.8239422E-02 at 140iterations 2.5813400E-03 5.5282593E-02 at 150iterations 1.4375859E-03 3.5848618E-02 at 160iterations 8.0294063E-04 1.7436981E-02 at 170iterations 4.4947784E-04 9.0560913E-03 at 180iterations finished qdiffx linear iterations at : 08:22:02 total time elapsed so far: 16.90000 # loops : 180 mean,max change (kT/e) : 4.4947784E-04 9.0560913E-03 energy calculations done at 16.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.13000 DelPhi exited at 08:22:03 17.132u 0.368s 0:18.19 96.1% 0+0k 0+0io 0pf+0w