Tue Oct 11 08:36:29 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 08:36:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 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: 0.7495526 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): -9.120000 35.17000 ymin,ymax (A): -3.624000 34.05900 zmin,zma (A): 2.104000 49.59900 x,y,z range (A): 44.29000 37.68300 47.49500 scale (grids/A): 0.7495526 object centre (A): 13.02500 15.21750 25.85150 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 90.18047 89.53320 91.08300 assigned negative charge : -296.4602 centred at (gu) : 89.99104 89.58959 91.15017 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7848 nv = 96 ne = 84 npr = 40077 no. pairs analyzed = 40077 no. exposed pairs = 2430 no. arc points = 16712 no. surface atoms = 828 nbur = 1180 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 616 mr = 4603 m= 8 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1498 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7829572E-07 7.6236226E-08 midg,1,midg; midg,igrid,midg 2.2293374E-07 7.0499929E-08 1,midg,midg; igrid,midg,midg -7.5992681E-08 3.6485253E-07 gauss-seidel spectral radius is 0.9907080 estimated iterations to convergence 84 setup time was (sec) 0.5100000 now iterating at: 08:36:29 rms-change max change #iterations 0.2433585 34.69327 at 10iterations 3.3688940E-02 4.071243 at 20iterations 4.7805710E-03 0.7148914 at 30iterations 7.2239264E-04 8.9004397E-02 at 40iterations 1.3700918E-04 1.5226364E-02 at 50iterations finished qdiffx linear iterations at : 08:36:32 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.3700918E-04 1.5226364E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:36:32 3.355u 0.129s 0:03.77 92.0% 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 08:36:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 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: 2.248658 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): -9.120000 35.17000 ymin,ymax (A): -3.624000 34.05900 zmin,zma (A): 2.104000 49.59900 x,y,z range (A): 44.29000 37.68300 47.49500 scale (grids/A): 2.248658 object centre (A): 13.02500 15.21750 25.85150 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 90.54146 88.59978 93.24909 assigned negative charge : -296.4602 centred at (gu) : 89.97339 88.76877 93.45084 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16712 grid for indexing accessible points = 1.400000 m= 35657 mr = 59173 m= 7950 mr = 27781 m= 881 mr = 5558 m= 30 mr = 495 m= 0 mr = 3 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 34122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14997 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) : 0.7495526 object centre at (A) : 13.02500 15.21750 25.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2751479E-02 1.4639462E-02 midg,1,midg; midg,igrid,midg 4.5378067E-02 1.1801446E-02 1,midg,midg; igrid,midg,midg 3.4462977E-02 6.6879600E-02 gauss-seidel spectral radius is 0.9989354 estimated iterations to convergence 242 setup time was (sec) 0.9300000 now iterating at: 08:36:34 rms-change max change #iterations 4.942190 177.6755 at 10iterations 2.541175 86.73684 at 20iterations 1.300791 40.73450 at 30iterations 0.6691873 21.61439 at 40iterations 0.3446192 10.31128 at 50iterations 0.1770905 5.916481 at 60iterations 9.0985417E-02 2.588324 at 70iterations 4.6479706E-02 1.251553 at 80iterations 2.3922933E-02 0.6355438 at 90iterations 1.2351763E-02 0.3473082 at 100iterations 6.3904887E-03 0.1707611 at 110iterations 3.3203848E-03 9.3032837E-02 at 120iterations finished qdiffx linear iterations at : 08:36:40 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 3.3203848E-03 9.3032837E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 08:36:41 7.656u 0.184s 0:08.27 94.6% 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 08:36:41 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 = 2008 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: 3.372987 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): -9.120000 35.17000 ymin,ymax (A): -3.624000 34.05900 zmin,zma (A): 2.104000 49.59900 x,y,z range (A): 44.29000 37.68300 47.49500 scale (grids/A): 3.372987 object centre (A): 13.02500 15.21750 25.85150 number of atom coordinates read : 2008 total number of charged atoms : 1880 net assigned charge : 6.500006 assigned positive charge : 302.9601 centred at (gu) : 90.81214 87.89960 94.87373 assigned negative charge : -296.4602 centred at (gu) : 89.96024 88.15324 95.17635 start vw surface at 0.1400000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 189915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16712 grid for indexing accessible points = 1.400000 m= 107721 mr = 141673 m= 48044 mr = 90938 m= 15531 mr = 40333 m= 3555 mr = 12409 m= 536 mr = 2633 m= 19 mr = 381 m= 0 mr = 5 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 76949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 15040 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) : 2.248658 object centre at (A) : 13.02500 15.21750 25.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4874324 5.1537242E-02 midg,1,midg; midg,igrid,midg 0.3537300 7.8178465E-02 1,midg,midg; igrid,midg,midg 0.4970810 0.4747460 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 2.370000 now iterating at: 08:36:43 rms-change max change #iterations 10.73234 261.7643 at 10iterations 6.431970 124.0161 at 20iterations 3.834912 68.04374 at 30iterations 2.285996 42.21331 at 40iterations 1.356870 24.07639 at 50iterations 0.8063615 15.19915 at 60iterations 0.4785056 8.993928 at 70iterations 0.2834188 4.990557 at 80iterations 0.1677257 2.730820 at 90iterations 9.9228784E-02 1.575186 at 100iterations 5.8799498E-02 0.9589443 at 110iterations 3.4876972E-02 0.6637554 at 120iterations 2.0723628E-02 0.3446071 at 130iterations 1.2413205E-02 0.2090740 at 140iterations 7.5441990E-03 0.1257706 at 150iterations 4.7050612E-03 7.8453064E-02 at 160iterations 3.0361244E-03 5.1681519E-02 at 170iterations 2.0772407E-03 3.3258438E-02 at 180iterations finished qdiffx linear iterations at : 08:36:54 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 2.0772407E-03 3.3258438E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 08:36:54 12.824u 0.204s 0:13.41 97.0% 0+0k 0+0io 0pf+0w