Sat Oct 8 11:36:13 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 Sat Oct 8 2011 at 11:36:13 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4326 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5728262 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): -27.06100 35.08700 ymin,ymax (A): 37.72200 98.08300 zmin,zma (A): 30.81500 90.03100 x,y,z range (A): 62.14799 60.36100 59.21600 scale (grids/A): 0.5728262 object centre (A): 4.013000 67.90250 60.42300 number of atom coordinates read : 4326 total number of charged atoms : 4167 net assigned charge : -2.485949 assigned positive charge : 648.6375 centred at (gu) : 90.67656 87.81966 88.78888 assigned negative charge : -651.1266 centred at (gu) : 90.58319 87.94170 88.96239 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9007 nv = 96 ne = 84 npr = 91356 no. pairs analyzed = 91356 no. exposed pairs = 4920 no. arc points = 33095 no. surface atoms = 1668 nbur = 2658 mkacc time = 0.2400000 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 = 1.484000 m= 390 mr = 5207 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.4700000 number of dielectric boundary points 4163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3452 ## 375 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9914455E-09 -3.7644128E-09 midg,1,midg; midg,igrid,midg 4.2151655E-09 -2.1978193E-09 1,midg,midg; igrid,midg,midg -2.5032723E-09 2.0776025E-09 gauss-seidel spectral radius is 0.9843675 estimated iterations to convergence 66 setup time was (sec) 0.8100000 now iterating at: 11:36:14 rms-change max change #iterations 0.1151354 19.83208 at 10iterations 9.2007909E-03 1.310409 at 20iterations 1.1920026E-03 0.1706314 at 30iterations 3.1073659E-04 4.3376923E-02 at 40iterations 1.0337857E-04 1.1685133E-02 at 50iterations finished qdiffx linear iterations at : 11:36:19 total time elapsed so far: 5.220000 # loops : 50 mean,max change (kT/e) : 1.0337857E-04 1.1685133E-02 energy calculations done at 5.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.390000 DelPhi exited at 11:36:19 5.391u 0.491s 0:06.16 95.4% 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 Sat Oct 8 2011 at 11:36:19 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4326 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.718479 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): -27.06100 35.08700 ymin,ymax (A): 37.72200 98.08300 zmin,zma (A): 30.81500 90.03100 x,y,z range (A): 62.14799 60.36100 59.21600 scale (grids/A): 1.718479 object centre (A): 4.013000 67.90250 60.42300 number of atom coordinates read : 4326 total number of charged atoms : 4167 net assigned charge : -2.485949 assigned positive charge : 648.6375 centred at (gu) : 92.02820 83.45775 86.36514 assigned negative charge : -651.1266 centred at (gu) : 91.74885 83.82486 86.88657 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 101117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33095 grid for indexing accessible points = 1.400000 m= 34480 mr = 73437 m= 4159 mr = 25297 m= 144 mr = 2463 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6274 time to turn everything in is 0.9500000 number of dielectric boundary points 38681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 32299 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) : 0.5728262 object centre at (A) : 4.013000 67.90250 60.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4555999E-02 -2.4289226E-02 midg,1,midg; midg,igrid,midg 4.1458569E-02 -5.7945116E-03 1,midg,midg; igrid,midg,midg -2.1474242E-02 3.0179301E-02 gauss-seidel spectral radius is 0.9984764 estimated iterations to convergence 203 setup time was (sec) 1.350000 now iterating at: 11:36:21 rms-change max change #iterations 4.613740 158.4510 at 10iterations 2.071567 68.17465 at 20iterations 0.9308934 24.65525 at 30iterations 0.4195589 12.20605 at 40iterations 0.1882274 5.027016 at 50iterations 8.4694110E-02 2.489838 at 60iterations 3.8119201E-02 1.028856 at 70iterations 1.7253162E-02 0.5080676 at 80iterations 7.8105284E-03 0.2187929 at 90iterations 3.5766629E-03 0.1048799 at 100iterations 1.6590786E-03 5.0240517E-02 at 110iterations 7.9514552E-04 2.1575928E-02 at 120iterations finished qdiffx linear iterations at : 11:36:33 total time elapsed so far: 12.87000 # loops : 120 mean,max change (kT/e) : 7.9514552E-04 2.1575928E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 11:36:33 13.041u 0.558s 0:13.90 97.7% 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 Sat Oct 8 2011 at 11:36:33 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4326 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.577718 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): -27.06100 35.08700 ymin,ymax (A): 37.72200 98.08300 zmin,zma (A): 30.81500 90.03100 x,y,z range (A): 62.14799 60.36100 59.21600 scale (grids/A): 2.577718 object centre (A): 4.013000 67.90250 60.42300 number of atom coordinates read : 4326 total number of charged atoms : 4167 net assigned charge : -2.485949 assigned positive charge : 648.6375 centred at (gu) : 93.04195 80.18638 84.54745 assigned negative charge : -651.1266 centred at (gu) : 92.62339 80.73719 85.32990 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 235035 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33095 grid for indexing accessible points = 1.400000 m= 116527 mr = 178158 m= 36685 mr = 95928 m= 7199 mr = 29159 m= 692 mr = 5262 m= 15 mr = 395 m= 0 mr = 4 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 21328 time to turn everything in is 2.160000 number of dielectric boundary points 87247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 33326 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) : 1.718479 object centre at (A) : 4.013000 67.90250 60.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7185860 -0.2909794 midg,1,midg; midg,igrid,midg 0.5870827 -6.6882782E-02 1,midg,midg; igrid,midg,midg -0.2957614 0.3085121 gauss-seidel spectral radius is 0.9992413 estimated iterations to convergence 287 setup time was (sec) 2.580000 now iterating at: 11:36:36 rms-change max change #iterations 11.31677 309.0576 at 10iterations 6.586566 131.9245 at 20iterations 3.809690 74.22037 at 30iterations 2.201962 40.26005 at 40iterations 1.264472 22.34648 at 50iterations 0.7278575 11.90108 at 60iterations 0.4180747 7.063902 at 70iterations 0.2392905 4.135451 at 80iterations 0.1369202 2.159805 at 90iterations 7.8384005E-02 1.383530 at 100iterations 4.4943675E-02 0.7018571 at 110iterations 2.5728181E-02 0.4689178 at 120iterations 1.4736723E-02 0.2378368 at 130iterations 8.4569743E-03 0.1366310 at 140iterations 4.8785987E-03 8.9163780E-02 at 150iterations 2.8367534E-03 5.1170349E-02 at 160iterations 1.6706153E-03 2.6790619E-02 at 170iterations 1.0059025E-03 1.6616821E-02 at 180iterations finished qdiffx linear iterations at : 11:36:56 total time elapsed so far: 22.63000 # loops : 180 mean,max change (kT/e) : 1.0059025E-03 1.6616821E-02 energy calculations done at 22.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.80000 DelPhi exited at 11:36:57 22.803u 0.544s 0:23.67 98.6% 0+0k 0+0io 0pf+0w