Tue Oct 11 08:10:10 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 Tue Oct 11 2011 at 08:10:11 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1178 !!! WARNING: HIZ 320 has a net charge of 0.2000 !!! WARNING: ZN3 355 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8283308 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): -38.20000 3.353000 ymin,ymax (A): -46.44300 -3.465000 zmin,zma (A): -24.35800 12.78200 x,y,z range (A): 41.55300 42.97800 37.14000 scale (grids/A): 0.8283308 object centre (A): -17.42350 -24.95400 -5.788000 number of atom coordinates read : 1178 total number of charged atoms : 1045 net assigned charge : 0.1000056 assigned positive charge : 167.2771 centred at (gu) : 89.86494 86.89452 91.27695 assigned negative charge : -167.1771 centred at (gu) : 89.83276 86.99467 91.58848 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5460 nv = 96 ne = 84 npr = 24542 no. pairs analyzed = 24542 no. exposed pairs = 1539 no. arc points = 10938 no. surface atoms = 520 nbur = 658 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 2865 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.1700000 number of dielectric boundary points 2948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 621 ## 40 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 5017 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5065251E-07 -1.0352594E-06 midg,1,midg; midg,igrid,midg 4.7617411E-07 -1.4772495E-07 1,midg,midg; igrid,midg,midg -7.2498892E-08 9.6048481E-08 gauss-seidel spectral radius is 0.9922951 estimated iterations to convergence 92 setup time was (sec) 0.4400000 now iterating at: 08:10:11 rms-change max change #iterations 0.2925805 44.96452 at 10iterations 4.7783673E-02 7.114342 at 20iterations 7.8200437E-03 1.242111 at 30iterations 1.2832262E-03 0.1963749 at 40iterations 2.0928582E-04 3.0170441E-02 at 50iterations finished qdiffx linear iterations at : 08:10:16 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 2.0928582E-04 3.0170441E-02 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 08:10:16 4.777u 0.385s 0:05.57 92.4% 0+0k 0+0io 6pf+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 08:10:16 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1178 !!! WARNING: HIZ 320 has a net charge of 0.2000 !!! WARNING: ZN3 355 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.484993 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): -38.20000 3.353000 ymin,ymax (A): -46.44300 -3.465000 zmin,zma (A): -24.35800 12.78200 x,y,z range (A): 41.55300 42.97800 37.14000 scale (grids/A): 2.484993 object centre (A): -17.42350 -24.95400 -5.788000 number of atom coordinates read : 1178 total number of charged atoms : 1045 net assigned charge : 0.1000056 assigned positive charge : 167.2771 centred at (gu) : 89.59494 80.68365 93.83102 assigned negative charge : -167.1771 centred at (gu) : 89.49823 80.98415 94.76547 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 56518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10938 grid for indexing accessible points = 1.400000 m= 21711 mr = 36970 m= 5292 mr = 16224 m= 677 mr = 3762 m= 30 mr = 377 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1720 time to turn everything in is 0.5100000 number of dielectric boundary points 26886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 8346 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) : 0.8283308 object centre at (A) : -17.42350 -24.95400 -5.788000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7759313E-02 -3.5184868E-02 midg,1,midg; midg,igrid,midg -3.3640806E-02 -1.2676671E-02 1,midg,midg; igrid,midg,midg -2.1297485E-05 -1.7426480E-02 gauss-seidel spectral radius is 0.9990205 estimated iterations to convergence 253 setup time was (sec) 0.8200000 now iterating at: 08:10:17 rms-change max change #iterations 4.400547 239.1751 at 10iterations 2.303191 82.51260 at 20iterations 1.210045 38.26232 at 30iterations 0.6330672 19.43894 at 40iterations 0.3334347 10.89302 at 50iterations 0.1744161 5.681942 at 60iterations 9.1874123E-02 3.229485 at 70iterations 4.8179343E-02 1.624893 at 80iterations 2.5233084E-02 0.8559780 at 90iterations 1.3260566E-02 0.4529123 at 100iterations 6.9542732E-03 0.2439537 at 110iterations 3.6570886E-03 0.1188574 at 120iterations finished qdiffx linear iterations at : 08:10:29 total time elapsed so far: 12.15000 # loops : 120 mean,max change (kT/e) : 3.6570886E-03 0.1188574 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 08:10:29 12.312u 0.457s 0:13.32 95.7% 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 08:10:29 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1178 !!! WARNING: HIZ 320 has a net charge of 0.2000 !!! WARNING: ZN3 355 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.727489 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): -38.20000 3.353000 ymin,ymax (A): -46.44300 -3.465000 zmin,zma (A): -24.35800 12.78200 x,y,z range (A): 41.55300 42.97800 37.14000 scale (grids/A): 3.727489 object centre (A): -17.42350 -24.95400 -5.788000 number of atom coordinates read : 1178 total number of charged atoms : 1045 net assigned charge : 0.1000056 assigned positive charge : 167.2771 centred at (gu) : 89.39254 76.02551 95.74646 assigned negative charge : -167.1771 centred at (gu) : 89.24732 76.47622 97.14828 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 130164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10938 grid for indexing accessible points = 1.400000 m= 65305 mr = 89590 m= 29572 mr = 53118 m= 10316 mr = 24625 m= 2621 mr = 8219 m= 407 mr = 1959 m= 37 mr = 284 m= 0 mr = 16 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 5536 time to turn everything in is 1.590000 number of dielectric boundary points 60611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 8360 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) : 2.484993 object centre at (A) : -17.42350 -24.95400 -5.788000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4637603 -0.2709765 midg,1,midg; midg,igrid,midg -0.1150413 -2.2449100E-02 1,midg,midg; igrid,midg,midg 9.9851027E-02 -0.2610204 gauss-seidel spectral radius is 0.9993373 estimated iterations to convergence 306 setup time was (sec) 1.900000 now iterating at: 08:10:32 rms-change max change #iterations 9.096112 242.3435 at 10iterations 5.387818 130.3628 at 20iterations 3.182430 66.20768 at 30iterations 1.879866 36.39975 at 40iterations 1.112633 20.10709 at 50iterations 0.6553859 12.09612 at 60iterations 0.3870659 6.893974 at 70iterations 0.2288473 4.024518 at 80iterations 0.1347117 2.386276 at 90iterations 7.9823591E-02 1.539585 at 100iterations 4.7009140E-02 0.9045639 at 110iterations 2.7716976E-02 0.5042267 at 120iterations 1.6398974E-02 0.2884531 at 130iterations 9.7058769E-03 0.1758728 at 140iterations 5.7195341E-03 0.1150341 at 150iterations 3.3899110E-03 6.6057682E-02 at 160iterations 2.0020148E-03 3.5803080E-02 at 170iterations 1.1856385E-03 2.1102905E-02 at 180iterations finished qdiffx linear iterations at : 08:10:51 total time elapsed so far: 20.76000 # loops : 180 mean,max change (kT/e) : 1.1856385E-03 2.1102905E-02 energy calculations done at 20.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.91000 DelPhi exited at 08:10:51 20.914u 0.529s 0:21.99 97.4% 0+0k 0+0io 0pf+0w