Mon Oct 10 17:01:44 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 Mon Oct 10 2011 at 17:01:44 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4312 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5147260 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): -16.04000 36.49900 ymin,ymax (A): -32.19100 31.28400 zmin,zma (A): -3.638000 65.52500 x,y,z range (A): 52.53900 63.47500 69.16300 scale (grids/A): 0.5147260 object centre (A): 10.22950 -0.4534988 30.94350 number of atom coordinates read : 4312 total number of charged atoms : 4110 net assigned charge : 0.9000361 assigned positive charge : 646.2403 centred at (gu) : 90.35678 90.74840 87.59507 assigned negative charge : -645.3442 centred at (gu) : 90.24342 90.80211 87.72031 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7152 nv = 96 ne = 84 npr = 88261 no. pairs analyzed = 88261 no. exposed pairs = 5591 no. arc points = 39015 no. surface atoms = 1864 nbur = 2448 mkacc time = 0.1800000 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 = 1.652000 m= 245 mr = 3582 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3765 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6369699E-10 -1.8435196E-10 midg,1,midg; midg,igrid,midg 1.2649312E-10 -1.7559082E-10 1,midg,midg; igrid,midg,midg -2.8436989E-10 3.4706282E-10 gauss-seidel spectral radius is 0.9806618 estimated iterations to convergence 59 setup time was (sec) 0.6300000 now iterating at: 17:01:45 rms-change max change #iterations 6.7173496E-02 10.68898 at 10iterations 3.8803832E-03 0.5367889 at 20iterations 2.8538782E-04 4.6585083E-02 at 30iterations 6.0423579E-05 7.7567101E-03 at 40iterations 1.9597239E-05 2.5327206E-03 at 50iterations finished qdiffx linear iterations at : 17:01:47 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.9597239E-05 2.5327206E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 17:01:48 3.279u 0.136s 0:04.24 80.1% 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 Mon Oct 10 2011 at 17:01:48 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4312 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.544178 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): -16.04000 36.49900 ymin,ymax (A): -32.19100 31.28400 zmin,zma (A): -3.638000 65.52500 x,y,z range (A): 52.53900 63.47500 69.16300 scale (grids/A): 1.544178 object centre (A): 10.22950 -0.4534988 30.94350 number of atom coordinates read : 4312 total number of charged atoms : 4110 net assigned charge : 0.9000361 assigned positive charge : 646.2403 centred at (gu) : 91.06942 92.24383 82.78381 assigned negative charge : -645.3442 centred at (gu) : 90.72996 92.40618 83.16068 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39015 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22622 mr = 54442 m= 1983 mr = 14601 m= 56 mr = 827 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.6000000 number of dielectric boundary points 35433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 30974 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) : 0.5147260 object centre at (A) : 10.22950 -0.4534988 30.94350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0695391E-03 -1.3830396E-02 midg,1,midg; midg,igrid,midg -1.1652234E-03 -6.8928692E-03 1,midg,midg; igrid,midg,midg -2.7160652E-03 9.0752542E-03 gauss-seidel spectral radius is 0.9980984 estimated iterations to convergence 182 setup time was (sec) 0.8800000 now iterating at: 17:01:50 rms-change max change #iterations 3.620163 159.8945 at 10iterations 1.472542 54.57499 at 20iterations 0.6009645 20.88130 at 30iterations 0.2464264 7.953879 at 40iterations 0.1001981 3.329009 at 50iterations 4.1138548E-02 1.483467 at 60iterations 1.6809054E-02 0.5531559 at 70iterations 6.8848305E-03 0.2411175 at 80iterations 2.8237992E-03 8.9594126E-02 at 90iterations 1.1611254E-03 4.0741444E-02 at 100iterations 4.7970624E-04 1.5321732E-02 at 110iterations 2.0189812E-04 6.6184998E-03 at 120iterations finished qdiffx linear iterations at : 17:01:56 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 2.0189812E-04 6.6184998E-03 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 17:01:57 7.371u 0.274s 0:08.76 87.2% 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 Mon Oct 10 2011 at 17:01:58 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4312 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.316267 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): -16.04000 36.49900 ymin,ymax (A): -32.19100 31.28400 zmin,zma (A): -3.638000 65.52500 x,y,z range (A): 52.53900 63.47500 69.16300 scale (grids/A): 2.316267 object centre (A): 10.22950 -0.4534988 30.94350 number of atom coordinates read : 4312 total number of charged atoms : 4110 net assigned charge : 0.9000361 assigned positive charge : 646.2403 centred at (gu) : 91.60380 93.36524 79.17550 assigned negative charge : -645.3442 centred at (gu) : 91.09478 93.60909 79.74097 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 187672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39015 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 81887 mr = 133989 m= 20137 mr = 63015 m= 2895 mr = 14007 m= 159 mr = 1747 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 544 time to turn everything in is 1.370000 number of dielectric boundary points 79948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 32811 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) : 1.544178 object centre at (A) : 10.22950 -0.4534988 30.94350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1702124 -0.2825871 midg,1,midg; midg,igrid,midg -7.6773562E-02 -0.1830944 1,midg,midg; igrid,midg,midg -3.8734961E-02 0.1220114 gauss-seidel spectral radius is 0.9991497 estimated iterations to convergence 271 setup time was (sec) 1.670000 now iterating at: 17:01:59 rms-change max change #iterations 9.836660 316.2611 at 10iterations 5.614254 145.7511 at 20iterations 3.183321 69.77636 at 30iterations 1.794418 39.81093 at 40iterations 1.005706 23.10426 at 50iterations 0.5629264 12.22878 at 60iterations 0.3133169 6.516245 at 70iterations 0.1748239 3.921840 at 80iterations 9.7076386E-02 2.234807 at 90iterations 5.3882878E-02 1.139356 at 100iterations 2.9945444E-02 0.9042168 at 110iterations 1.6609101E-02 0.4309416 at 120iterations 9.2079490E-03 0.1984520 at 130iterations 5.1113288E-03 0.1014066 at 140iterations 2.8286390E-03 5.5880070E-02 at 150iterations 1.5696400E-03 3.0746460E-02 at 160iterations 8.7253889E-04 1.7142296E-02 at 170iterations 4.8817851E-04 8.9440346E-03 at 180iterations finished qdiffx linear iterations at : 17:02:10 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 4.8817851E-04 8.9440346E-03 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 17:02:12 12.655u 0.280s 0:14.17 91.2% 0+0k 0+0io 0pf+0w