Sun Oct 9 00:38:23 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 9 2011 at 00:38:23 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 = 2442 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6184636 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): -13.19200 40.72400 ymin,ymax (A): -32.33900 25.22300 zmin,zma (A): -9.628000 33.59400 x,y,z range (A): 53.91600 57.56200 43.22200 scale (grids/A): 0.6184636 object centre (A): 13.76600 -3.558001 11.98300 number of atom coordinates read : 2442 total number of charged atoms : 2307 net assigned charge : 11.50002 assigned positive charge : 355.7192 centred at (gu) : 89.79002 91.38280 90.40570 assigned negative charge : -344.2199 centred at (gu) : 89.79042 91.38840 90.36720 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6325 nv = 96 ne = 84 npr = 48700 no. pairs analyzed = 48700 no. exposed pairs = 3199 no. arc points = 22909 no. surface atoms = 1070 nbur = 1372 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3280 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2800000 number of dielectric boundary points 3336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2286 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0947976E-09 1.1972816E-08 midg,1,midg; midg,igrid,midg 6.8070647E-09 1.1429406E-08 1,midg,midg; igrid,midg,midg 9.2375707E-09 8.4035410E-09 gauss-seidel spectral radius is 0.9864560 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 00:38:24 rms-change max change #iterations 0.1180421 17.57669 at 10iterations 1.0973309E-02 1.679088 at 20iterations 1.0994539E-03 0.1825161 at 30iterations 1.9497654E-04 3.8618088E-02 at 40iterations 5.8191941E-05 1.2881279E-02 at 50iterations finished qdiffx linear iterations at : 00:38:27 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 5.8191941E-05 1.2881279E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 00:38:28 4.084u 0.230s 0:04.59 93.8% 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 9 2011 at 00:38:28 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 = 2442 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.855391 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): -13.19200 40.72400 ymin,ymax (A): -32.33900 25.22300 zmin,zma (A): -9.628000 33.59400 x,y,z range (A): 53.91600 57.56200 43.22200 scale (grids/A): 1.855391 object centre (A): 13.76600 -3.558001 11.98300 number of atom coordinates read : 2442 total number of charged atoms : 2307 net assigned charge : 11.50002 assigned positive charge : 355.7192 centred at (gu) : 89.36948 94.14819 91.21665 assigned negative charge : -344.2199 centred at (gu) : 89.37128 94.16510 91.10180 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22909 grid for indexing accessible points = 1.400000 m= 22879 mr = 46010 m= 3313 mr = 16137 m= 152 mr = 1846 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1117 time to turn everything in is 0.5200000 number of dielectric boundary points 30896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18058 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) : 0.6184636 object centre at (A) : 13.76600 -3.558001 11.98300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8063104E-03 1.6633429E-02 midg,1,midg; midg,igrid,midg 3.3178784E-02 3.2239147E-02 1,midg,midg; igrid,midg,midg 3.5569064E-02 3.5625767E-02 gauss-seidel spectral radius is 0.9985580 estimated iterations to convergence 209 setup time was (sec) 0.8300000 now iterating at: 00:38:29 rms-change max change #iterations 3.808539 229.6988 at 10iterations 1.734604 62.23159 at 20iterations 0.7921807 30.89853 at 30iterations 0.3634430 13.09227 at 40iterations 0.1660322 6.172919 at 50iterations 7.6093808E-02 2.531780 at 60iterations 3.4916483E-02 1.148164 at 70iterations 1.6079271E-02 0.5187080 at 80iterations 7.3961802E-03 0.2434235 at 90iterations 3.4272433E-03 0.1149454 at 100iterations 1.6216771E-03 5.5580139E-02 at 110iterations 7.9729530E-04 3.5960197E-02 at 120iterations finished qdiffx linear iterations at : 00:38:37 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 7.9729530E-04 3.5960197E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 00:38:38 9.303u 0.254s 0:09.86 96.8% 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 9 2011 at 00:38:38 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 = 2442 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.783086 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): -13.19200 40.72400 ymin,ymax (A): -32.33900 25.22300 zmin,zma (A): -9.628000 33.59400 x,y,z range (A): 53.91600 57.56200 43.22200 scale (grids/A): 2.783086 object centre (A): 13.76600 -3.558001 11.98300 number of atom coordinates read : 2442 total number of charged atoms : 2307 net assigned charge : 11.50002 assigned positive charge : 355.7192 centred at (gu) : 89.05418 96.22212 91.82475 assigned negative charge : -344.2199 centred at (gu) : 89.05688 96.24763 91.65259 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 158686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22909 grid for indexing accessible points = 1.400000 m= 75847 mr = 112088 m= 25287 mr = 60376 m= 5611 mr = 19600 m= 748 mr = 3942 m= 26 mr = 488 m= 0 mr = 10 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 3508 time to turn everything in is 1.390000 number of dielectric boundary points 69701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18450 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) : 1.855391 object centre at (A) : 13.76600 -3.558001 11.98300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5578402E-02 0.1646246 midg,1,midg; midg,igrid,midg 0.4713434 0.3878952 1,midg,midg; igrid,midg,midg 0.3540124 0.4476383 gauss-seidel spectral radius is 0.9992416 estimated iterations to convergence 287 setup time was (sec) 1.730000 now iterating at: 00:38:40 rms-change max change #iterations 9.176299 314.0914 at 10iterations 5.359409 127.7494 at 20iterations 3.107494 66.79444 at 30iterations 1.801811 39.84549 at 40iterations 1.038140 21.47846 at 50iterations 0.5971719 12.90963 at 60iterations 0.3426595 6.743015 at 70iterations 0.1967957 3.959684 at 80iterations 0.1128857 2.179810 at 90iterations 6.4713329E-02 1.261133 at 100iterations 3.6985047E-02 0.8034639 at 110iterations 2.1131184E-02 0.4454956 at 120iterations 1.2121408E-02 0.2476149 at 130iterations 6.9441642E-03 0.1431293 at 140iterations 4.0065655E-03 8.5334778E-02 at 150iterations 2.3074278E-03 4.6779633E-02 at 160iterations 1.3488524E-03 3.0199051E-02 at 170iterations 8.1046176E-04 1.9065857E-02 at 180iterations finished qdiffx linear iterations at : 00:38:53 total time elapsed so far: 14.87000 # loops : 180 mean,max change (kT/e) : 8.1046176E-04 1.9065857E-02 energy calculations done at 14.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.06000 DelPhi exited at 00:38:53 15.059u 0.265s 0:15.62 98.0% 0+0k 0+0io 0pf+0w