Tue Oct 11 07:00:27 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 07:00:27 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3085 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 0.5521863 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): -60.42700 -2.406000 ymin,ymax (A): 2.163000 66.63400 zmin,zma (A): -32.25200 17.52400 x,y,z range (A): 58.02100 64.47100 49.77600 scale (grids/A): 0.5521863 object centre (A): -31.41650 34.39850 -7.363999 number of atom coordinates read : 3085 total number of charged atoms : 2940 net assigned charge : -2.099989 assigned positive charge : 454.0774 centred at (gu) : 90.87261 89.04336 90.24440 assigned negative charge : -456.1779 centred at (gu) : 90.67319 89.14474 90.28998 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6094 nv = 96 ne = 84 npr = 63772 no. pairs analyzed = 63772 no. exposed pairs = 3897 no. arc points = 27398 no. surface atoms = 1313 nbur = 1772 mkacc time = 0.1900000 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= 253 mr = 3202 m= 0 mr = 13 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3900000 number of dielectric boundary points 3132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2697 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7928 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8766912E-10 -6.1761546E-10 midg,1,midg; midg,igrid,midg 8.5343882E-10 -8.4451918E-10 1,midg,midg; igrid,midg,midg -1.5645907E-09 1.8423726E-09 gauss-seidel spectral radius is 0.9830980 estimated iterations to convergence 63 setup time was (sec) 0.6600000 now iterating at: 07:00:28 rms-change max change #iterations 7.9923414E-02 13.81891 at 10iterations 5.3899833E-03 0.9889984 at 20iterations 3.6776153E-04 6.1088562E-02 at 30iterations 2.6446194E-05 4.4174194E-03 at 40iterations 1.9591007E-06 3.2138824E-04 at 50iterations finished qdiffx linear iterations at : 07:00:32 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.9591007E-06 3.2138824E-04 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 07:00:33 4.177u 0.285s 0:05.13 86.7% 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 07:00:33 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3085 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.656559 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): -60.42700 -2.406000 ymin,ymax (A): 2.163000 66.63400 zmin,zma (A): -32.25200 17.52400 x,y,z range (A): 58.02100 64.47100 49.77600 scale (grids/A): 1.656559 object centre (A): -31.41650 34.39850 -7.363999 number of atom coordinates read : 3085 total number of charged atoms : 2940 net assigned charge : -2.099989 assigned positive charge : 454.0774 centred at (gu) : 92.61688 87.12912 90.73226 assigned negative charge : -456.1779 centred at (gu) : 92.01911 87.43373 90.86958 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 67506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27398 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21469 mr = 45788 m= 2368 mr = 15192 m= 64 mr = 1268 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1534 time to turn everything in is 0.6200000 number of dielectric boundary points 29154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22634 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) : 0.5521863 object centre at (A) : -31.41650 34.39850 -7.363999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1997810E-03 7.4969125E-03 midg,1,midg; midg,igrid,midg 1.4859663E-02 -3.8889963E-02 1,midg,midg; igrid,midg,midg -2.6620176E-02 7.1789543E-03 gauss-seidel spectral radius is 0.9982530 estimated iterations to convergence 190 setup time was (sec) 0.9300000 now iterating at: 07:00:34 rms-change max change #iterations 3.500864 191.2497 at 10iterations 1.486463 53.84791 at 20iterations 0.6325109 22.12387 at 30iterations 0.2666788 10.02029 at 40iterations 0.1135562 4.238422 at 50iterations 4.8159759E-02 1.693449 at 60iterations 2.0371970E-02 0.6978683 at 70iterations 8.6430656E-03 0.2793112 at 80iterations 3.6722033E-03 0.1306467 at 90iterations 1.5608498E-03 5.0938934E-02 at 100iterations 6.6027074E-04 2.2802353E-02 at 110iterations 2.8094367E-04 9.4947815E-03 at 120iterations finished qdiffx linear iterations at : 07:00:42 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.8094367E-04 9.4947815E-03 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 07:00:43 9.479u 0.294s 0:10.04 97.2% 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 07:00:43 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3085 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.484838 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): -60.42700 -2.406000 ymin,ymax (A): 2.163000 66.63400 zmin,zma (A): -32.25200 17.52400 x,y,z range (A): 58.02100 64.47100 49.77600 scale (grids/A): 2.484838 object centre (A): -31.41650 34.39850 -7.363999 number of atom coordinates read : 3085 total number of charged atoms : 2940 net assigned charge : -2.099989 assigned positive charge : 454.0774 centred at (gu) : 93.92535 85.69362 91.09832 assigned negative charge : -456.1779 centred at (gu) : 93.02850 86.15065 91.30431 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 156768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27398 grid for indexing accessible points = 1.400000 m= 73458 mr = 111806 m= 22086 mr = 58844 m= 3778 mr = 17137 m= 244 mr = 2608 m= 5 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 5149 time to turn everything in is 1.500000 number of dielectric boundary points 65843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 23505 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) : 1.656559 object centre at (A) : -31.41650 34.39850 -7.363999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1124918 0.1583556 midg,1,midg; midg,igrid,midg 0.2416900 -0.6959090 1,midg,midg; igrid,midg,midg -0.4506559 7.3065057E-02 gauss-seidel spectral radius is 0.9991623 estimated iterations to convergence 273 setup time was (sec) 1.820000 now iterating at: 07:00:45 rms-change max change #iterations 8.879483 387.2151 at 10iterations 4.964454 138.3407 at 20iterations 2.780478 66.32901 at 30iterations 1.551681 35.17598 at 40iterations 0.8648552 22.75651 at 50iterations 0.4796743 11.82259 at 60iterations 0.2666961 5.754558 at 70iterations 0.1481188 3.072730 at 80iterations 8.1975766E-02 1.729362 at 90iterations 4.5524657E-02 1.123451 at 100iterations 2.5177693E-02 0.5494733 at 110iterations 1.3951317E-02 0.2872427 at 120iterations 7.7281576E-03 0.1525955 at 130iterations 4.2839260E-03 9.0040207E-02 at 140iterations 2.3725803E-03 4.6461105E-02 at 150iterations 1.3109336E-03 2.5634766E-02 at 160iterations 7.2602485E-04 1.4836311E-02 at 170iterations 4.0211921E-04 8.0833435E-03 at 180iterations finished qdiffx linear iterations at : 07:00:59 total time elapsed so far: 15.52000 # loops : 180 mean,max change (kT/e) : 4.0211921E-04 8.0833435E-03 energy calculations done at 15.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.69000 DelPhi exited at 07:00:59 15.691u 0.335s 0:16.54 96.8% 0+0k 0+0io 0pf+0w