Sun Oct 16 14:29:25 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 Sun Oct 16 2011 at 14:29:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6382216 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): -0.1830000 53.16400 ymin,ymax (A): -16.48900 27.53400 zmin,zma (A): 28.60200 84.38200 x,y,z range (A): 53.34700 44.02300 55.78000 scale (grids/A): 0.6382216 object centre (A): 26.49050 5.522500 56.49200 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 9.000021 assigned positive charge : 323.7068 centred at (gu) : 90.93945 89.37685 89.20719 assigned negative charge : -314.7072 centred at (gu) : 90.90926 89.47943 89.17800 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6347 nv = 96 ne = 84 npr = 44569 no. pairs analyzed = 44569 no. exposed pairs = 2959 no. arc points = 21540 no. surface atoms = 998 nbur = 1244 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3290 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2118 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7475 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1441731E-08 1.2702950E-08 midg,1,midg; midg,igrid,midg 2.4536625E-08 2.7248099E-09 1,midg,midg; igrid,midg,midg 7.9679685E-09 1.8362051E-08 gauss-seidel spectral radius is 0.9872614 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 14:29:31 rms-change max change #iterations 0.1286880 20.12590 at 10iterations 1.2665291E-02 2.415407 at 20iterations 1.2441804E-03 0.2060051 at 30iterations 1.3017947E-04 2.0622253E-02 at 40iterations 1.6246293E-05 2.5444031E-03 at 50iterations finished qdiffx linear iterations at : 14:29:41 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.6246293E-05 2.5444031E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 14:29:44 3.969u 0.165s 0:16.62 24.7% 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 Sun Oct 16 2011 at 14:29:46 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 = 2242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.914665 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): -0.1830000 53.16400 ymin,ymax (A): -16.48900 27.53400 zmin,zma (A): 28.60200 84.38200 x,y,z range (A): 53.34700 44.02300 55.78000 scale (grids/A): 1.914665 object centre (A): 26.49050 5.522500 56.49200 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 9.000021 assigned positive charge : 323.7068 centred at (gu) : 92.81831 88.13050 87.62150 assigned negative charge : -314.7072 centred at (gu) : 92.72812 88.43829 87.53406 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21540 grid for indexing accessible points = 1.400000 m= 23997 mr = 45314 m= 3881 mr = 17012 m= 278 mr = 2286 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 16588 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) : 0.6382216 object centre at (A) : 26.49050 5.522500 56.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7718272E-02 4.3777939E-02 midg,1,midg; midg,igrid,midg 2.3914635E-02 -5.7698041E-03 1,midg,midg; igrid,midg,midg 3.5862803E-02 4.3204393E-02 gauss-seidel spectral radius is 0.9986254 estimated iterations to convergence 214 setup time was (sec) 0.9700000 now iterating at: 14:29:52 rms-change max change #iterations 3.809912 189.8102 at 10iterations 1.773291 65.56492 at 20iterations 0.8287879 30.54993 at 30iterations 0.3846546 13.25655 at 40iterations 0.1798855 5.918769 at 50iterations 8.3660170E-02 2.847666 at 60iterations 3.9064817E-02 1.352901 at 70iterations 1.8186785E-02 0.5738163 at 80iterations 8.4921839E-03 0.2720089 at 90iterations 3.9553950E-03 0.1325989 at 100iterations 1.8541431E-03 6.2594414E-02 at 110iterations 8.6194009E-04 2.8222084E-02 at 120iterations finished qdiffx linear iterations at : 14:30:16 total time elapsed so far: 8.660000 # loops : 120 mean,max change (kT/e) : 8.6194009E-04 2.8222084E-02 energy calculations done at 8.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 14:30:19 8.877u 0.178s 0:33.73 26.8% 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 Sun Oct 16 2011 at 14:30:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.871997 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): -0.1830000 53.16400 ymin,ymax (A): -16.48900 27.53400 zmin,zma (A): 28.60200 84.38200 x,y,z range (A): 53.34700 44.02300 55.78000 scale (grids/A): 2.871997 object centre (A): 26.49050 5.522500 56.49200 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 9.000021 assigned positive charge : 323.7068 centred at (gu) : 94.22736 87.19569 86.43223 assigned negative charge : -314.7072 centred at (gu) : 94.09216 87.65751 86.30107 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 157003 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21540 grid for indexing accessible points = 1.400000 m= 77378 mr = 110103 m= 27902 mr = 61789 m= 6943 mr = 21781 m= 1130 mr = 4937 m= 73 mr = 722 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 71074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 16863 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) : 1.914665 object centre at (A) : 26.49050 5.522500 56.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3414822 0.6649848 midg,1,midg; midg,igrid,midg 0.2394704 -5.7492632E-02 1,midg,midg; igrid,midg,midg 0.3818214 0.4039255 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 1.960000 now iterating at: 14:30:32 rms-change max change #iterations 9.133765 411.9944 at 10iterations 5.365163 146.5902 at 20iterations 3.119525 78.90218 at 30iterations 1.806822 38.08390 at 40iterations 1.048325 21.47325 at 50iterations 0.6042287 13.35109 at 60iterations 0.3487542 6.874928 at 70iterations 0.2006833 3.899303 at 80iterations 0.1154619 2.202299 at 90iterations 6.6404305E-02 1.337642 at 100iterations 3.8196433E-02 0.7265625 at 110iterations 2.1921299E-02 0.4214458 at 120iterations 1.2623533E-02 0.2485008 at 130iterations 7.2429990E-03 0.1375496 at 140iterations 4.1585295E-03 7.9813004E-02 at 150iterations 2.3894454E-03 4.5601845E-02 at 160iterations 1.3703109E-03 2.5979042E-02 at 170iterations 7.8909233E-04 1.4298439E-02 at 180iterations finished qdiffx linear iterations at : 14:31:14 total time elapsed so far: 14.30000 # loops : 180 mean,max change (kT/e) : 7.8909233E-04 1.4298439E-02 energy calculations done at 14.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.53000 DelPhi exited at 14:31:18 14.530u 0.212s 0:55.05 26.7% 0+0k 0+0io 0pf+0w