Tue Oct 11 06:56:00 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 Tue Oct 11 2011 at 06:56:00 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 = 3003 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: 0.5775471 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): -19.89700 41.74300 ymin,ymax (A): 21.15600 76.91500 zmin,zma (A): -71.77700 -25.04200 x,y,z range (A): 61.64000 55.75900 46.73500 scale (grids/A): 0.5775471 object centre (A): 10.92300 49.03550 -48.40950 number of atom coordinates read : 3003 total number of charged atoms : 2864 net assigned charge : 2.500033 assigned positive charge : 440.5095 centred at (gu) : 89.97256 90.32894 90.33061 assigned negative charge : -438.0102 centred at (gu) : 89.86985 90.46282 90.31268 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6582 nv = 96 ne = 84 npr = 61767 no. pairs analyzed = 61767 no. exposed pairs = 3721 no. arc points = 26672 no. surface atoms = 1259 nbur = 1744 mkacc time = 0.1300000 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= 352 mr = 3533 m= 0 mr = 27 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3200000 number of dielectric boundary points 3374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2700 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4459024E-10 9.4163088E-10 midg,1,midg; midg,igrid,midg 2.9134315E-09 -2.3909792E-09 1,midg,midg; igrid,midg,midg -1.5764516E-09 2.5268523E-09 gauss-seidel spectral radius is 0.9845327 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 06:56:01 rms-change max change #iterations 9.5892221E-02 13.39201 at 10iterations 7.8785643E-03 1.333138 at 20iterations 6.9718150E-04 0.1201019 at 30iterations 8.5086307E-05 1.6891479E-02 at 40iterations 1.3674693E-05 2.9029846E-03 at 50iterations finished qdiffx linear iterations at : 06:56:03 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.3674693E-05 2.9029846E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:56:04 3.333u 0.186s 0:03.85 91.1% 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 06:56:04 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 = 3003 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: 1.732641 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): -19.89700 41.74300 ymin,ymax (A): 21.15600 76.91500 zmin,zma (A): -71.77700 -25.04200 x,y,z range (A): 61.64000 55.75900 46.73500 scale (grids/A): 1.732641 object centre (A): 10.92300 49.03550 -48.40950 number of atom coordinates read : 3003 total number of charged atoms : 2864 net assigned charge : 2.500033 assigned positive charge : 440.5095 centred at (gu) : 89.91682 90.98634 90.99124 assigned negative charge : -438.0102 centred at (gu) : 89.60933 91.38832 90.93760 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26672 grid for indexing accessible points = 1.400000 m= 26244 mr = 48271 m= 3865 mr = 19470 m= 130 mr = 2375 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 491 time to turn everything in is 0.5200000 number of dielectric boundary points 31240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 22260 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) : 0.5775471 object centre at (A) : 10.92300 49.03550 -48.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4368374E-03 1.9210862E-02 midg,1,midg; midg,igrid,midg 2.1884330E-03 -2.6546908E-03 1,midg,midg; igrid,midg,midg -5.5272882E-03 2.2486646E-02 gauss-seidel spectral radius is 0.9984033 estimated iterations to convergence 199 setup time was (sec) 0.8200000 now iterating at: 06:56:05 rms-change max change #iterations 3.753750 176.1957 at 10iterations 1.651056 67.17789 at 20iterations 0.7262223 24.60538 at 30iterations 0.3210840 10.13055 at 40iterations 0.1410101 4.710359 at 50iterations 6.2331486E-02 2.150375 at 60iterations 2.7568698E-02 0.9710274 at 70iterations 1.2230345E-02 0.4251814 at 80iterations 5.3844112E-03 0.1735249 at 90iterations 2.3959961E-03 9.8888397E-02 at 100iterations 1.0723316E-03 3.5366058E-02 at 110iterations 4.7941547E-04 1.6250610E-02 at 120iterations finished qdiffx linear iterations at : 06:56:11 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 4.7941547E-04 1.6250610E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 06:56:12 7.449u 0.204s 0:08.09 94.4% 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 Tue Oct 11 2011 at 06:56:12 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 = 3003 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: 2.598962 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): -19.89700 41.74300 ymin,ymax (A): 21.15600 76.91500 zmin,zma (A): -71.77700 -25.04200 x,y,z range (A): 61.64000 55.75900 46.73500 scale (grids/A): 2.598962 object centre (A): 10.92300 49.03550 -48.40950 number of atom coordinates read : 3003 total number of charged atoms : 2864 net assigned charge : 2.500033 assigned positive charge : 440.5095 centred at (gu) : 89.87481 91.47918 91.48680 assigned negative charge : -438.0102 centred at (gu) : 89.41376 92.08252 91.40630 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 164435 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26672 grid for indexing accessible points = 1.400000 m= 84124 mr = 117226 m= 30991 mr = 68521 m= 6742 mr = 25098 m= 638 mr = 5072 m= 23 mr = 385 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 1747 time to turn everything in is 1.250000 number of dielectric boundary points 70649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 22904 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) : 1.732641 object centre at (A) : 10.92300 49.03550 -48.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1017257 0.3047532 midg,1,midg; midg,igrid,midg 3.9853580E-02 -1.8798651E-02 1,midg,midg; igrid,midg,midg -0.1223448 0.4955300 gauss-seidel spectral radius is 0.9992048 estimated iterations to convergence 280 setup time was (sec) 1.550000 now iterating at: 06:56:14 rms-change max change #iterations 9.270419 276.8698 at 10iterations 5.318002 136.4485 at 20iterations 3.023766 69.78853 at 30iterations 1.718474 39.04971 at 40iterations 0.9761809 19.90248 at 50iterations 0.5513325 12.15613 at 60iterations 0.3111624 5.999348 at 70iterations 0.1753032 3.649331 at 80iterations 9.9035434E-02 2.168440 at 90iterations 5.5797145E-02 1.217571 at 100iterations 3.1407367E-02 0.6074142 at 110iterations 1.7674970E-02 0.4071474 at 120iterations 9.9443039E-03 0.1867018 at 130iterations 5.6004967E-03 0.1075888 at 140iterations 3.1564019E-03 6.2454700E-02 at 150iterations 1.7861746E-03 3.5055161E-02 at 160iterations 1.0092467E-03 1.9317627E-02 at 170iterations 5.7388609E-04 1.0845184E-02 at 180iterations finished qdiffx linear iterations at : 06:56:25 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 5.7388609E-04 1.0845184E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 06:56:26 13.228u 0.226s 0:13.77 97.6% 0+0k 0+0io 0pf+0w