Tue Oct 11 08:23:11 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 08:23:11 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2547 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 0.5638264 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): 17.82900 80.96900 ymin,ymax (A): -13.08000 39.56800 zmin,zma (A): -8.150000 34.62500 x,y,z range (A): 63.14000 52.64800 42.77500 scale (grids/A): 0.5638264 object centre (A): 49.39900 13.24400 13.23750 number of atom coordinates read : 2547 total number of charged atoms : 2400 net assigned charge : 8.312028 assigned positive charge : 380.1179 centred at (gu) : 87.56307 91.10368 89.98685 assigned negative charge : -371.8065 centred at (gu) : 87.74986 91.21206 90.08713 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5191 nv = 96 ne = 84 npr = 51124 no. pairs analyzed = 51124 no. exposed pairs = 3016 no. arc points = 21057 no. surface atoms = 1025 nbur = 1522 mkacc time = 0.1100000 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 = 1.540000 m= 227 mr = 2856 m= 0 mr = 20 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2900000 number of dielectric boundary points 2542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2105 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0221553E-09 -9.4603089E-11 midg,1,midg; midg,igrid,midg 1.6154788E-09 -2.5716065E-10 1,midg,midg; igrid,midg,midg 5.2457638E-09 -5.6036664E-10 gauss-seidel spectral radius is 0.9837340 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 08:23:12 rms-change max change #iterations 8.1275761E-02 13.53788 at 10iterations 7.1952674E-03 1.378654 at 20iterations 9.7280595E-04 0.2424622 at 30iterations 2.4198796E-04 6.5765381E-02 at 40iterations 6.6850145E-05 1.8051147E-02 at 50iterations finished qdiffx linear iterations at : 08:23:15 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 6.6850145E-05 1.8051147E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 08:23:15 3.094u 0.190s 0:03.91 83.8% 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 Tue Oct 11 2011 at 08:23:15 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2547 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 1.691479 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): 17.82900 80.96900 ymin,ymax (A): -13.08000 39.56800 zmin,zma (A): -8.150000 34.62500 x,y,z range (A): 63.14000 52.64800 42.77500 scale (grids/A): 1.691479 object centre (A): 49.39900 13.24400 13.23750 number of atom coordinates read : 2547 total number of charged atoms : 2400 net assigned charge : 8.312028 assigned positive charge : 380.1179 centred at (gu) : 82.68881 93.31051 89.95987 assigned negative charge : -371.8065 centred at (gu) : 83.24945 93.63594 90.26111 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21057 grid for indexing accessible points = 1.400000 m= 19534 mr = 40162 m= 2442 mr = 14445 m= 63 mr = 1433 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 712 time to turn everything in is 0.4100000 number of dielectric boundary points 23807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18485 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) : 0.5638264 object centre at (A) : 49.39900 13.24400 13.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3662256E-02 2.3527187E-03 midg,1,midg; midg,igrid,midg 1.0992073E-02 8.4742047E-03 1,midg,midg; igrid,midg,midg 1.4788992E-04 6.1115902E-03 gauss-seidel spectral radius is 0.9982576 estimated iterations to convergence 190 setup time was (sec) 0.6600000 now iterating at: 08:23:16 rms-change max change #iterations 3.246686 134.6620 at 10iterations 1.377427 53.29520 at 20iterations 0.5862528 24.56449 at 30iterations 0.2497461 8.883091 at 40iterations 0.1065884 3.935097 at 50iterations 4.5549031E-02 1.707138 at 60iterations 1.9443125E-02 0.7121792 at 70iterations 8.4112352E-03 0.3504591 at 80iterations 3.7181280E-03 0.1351662 at 90iterations 1.7222345E-03 7.0334435E-02 at 100iterations 8.4011134E-04 3.8265228E-02 at 110iterations 4.3755840E-04 2.3086548E-02 at 120iterations finished qdiffx linear iterations at : 08:23:22 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 4.3755840E-04 2.3086548E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 08:23:23 6.918u 0.171s 0:07.40 95.6% 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 08:23:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2547 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 2.537219 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): 17.82900 80.96900 ymin,ymax (A): -13.08000 39.56800 zmin,zma (A): -8.150000 34.62500 x,y,z range (A): 63.14000 52.64800 42.77500 scale (grids/A): 2.537219 object centre (A): 49.39900 13.24400 13.23750 number of atom coordinates read : 2547 total number of charged atoms : 2400 net assigned charge : 8.312028 assigned positive charge : 380.1179 centred at (gu) : 79.03294 94.96584 89.93970 assigned negative charge : -371.8065 centred at (gu) : 79.87408 95.45387 90.39162 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 134112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21057 grid for indexing accessible points = 1.400000 m= 65100 mr = 97459 m= 21323 mr = 53342 m= 4009 mr = 17223 m= 338 mr = 2999 m= 3 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2464 time to turn everything in is 0.9900000 number of dielectric boundary points 53686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 19192 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) : 1.691479 object centre at (A) : 49.39900 13.24400 13.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1660342 3.5523597E-02 midg,1,midg; midg,igrid,midg 0.1168258 0.1769939 1,midg,midg; igrid,midg,midg -0.2459724 9.0293758E-02 gauss-seidel spectral radius is 0.9991423 estimated iterations to convergence 270 setup time was (sec) 1.250000 now iterating at: 08:23:24 rms-change max change #iterations 8.074450 286.5093 at 10iterations 4.446689 128.9937 at 20iterations 2.459180 56.93453 at 30iterations 1.349007 29.50528 at 40iterations 0.7435379 15.55766 at 50iterations 0.4094798 9.132580 at 60iterations 0.2256766 4.967411 at 70iterations 0.1239250 2.673021 at 80iterations 6.8130508E-02 1.582428 at 90iterations 3.7611403E-02 0.9046593 at 100iterations 2.0784432E-02 0.4250355 at 110iterations 1.1503711E-02 0.2610817 at 120iterations 6.4277994E-03 0.1407623 at 130iterations 3.6514536E-03 9.2948914E-02 at 140iterations 2.1307839E-03 5.3737640E-02 at 150iterations 1.2840619E-03 3.4944534E-02 at 160iterations 8.0966204E-04 2.3902893E-02 at 170iterations 5.3676631E-04 1.5951157E-02 at 180iterations finished qdiffx linear iterations at : 08:23:34 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 5.3676631E-04 1.5951157E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 08:23:35 11.291u 0.168s 0:11.85 96.6% 0+0k 0+0io 0pf+0w