Mon Oct 10 14:01:43 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 Mon Oct 10 2011 at 14:01:43 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6395975 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): -11.86200 43.68800 ymin,ymax (A): -22.52500 22.34200 zmin,zma (A): -6.900000 48.76000 x,y,z range (A): 55.55000 44.86700 55.66000 scale (grids/A): 0.6395975 object centre (A): 15.91300 -9.1500282E-02 20.93000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 455.2846 centred at (gu) : 88.74108 89.69055 91.12917 assigned negative charge : -455.2713 centred at (gu) : 88.71956 89.59392 91.04897 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8178 nv = 96 ne = 84 npr = 63788 no. pairs analyzed = 63788 no. exposed pairs = 3452 no. arc points = 24061 no. surface atoms = 1166 nbur = 1865 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4796 m= 4 mr = 46 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 0.3500000 number of dielectric boundary points 3782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5608098E-09 1.3727203E-08 midg,1,midg; midg,igrid,midg -1.4126123E-08 1.2045979E-08 1,midg,midg; igrid,midg,midg -3.8678807E-09 2.1913635E-09 gauss-seidel spectral radius is 0.9873650 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:01:44 rms-change max change #iterations 0.1573096 23.71373 at 10iterations 1.5869249E-02 2.424286 at 20iterations 1.7530007E-03 0.2100391 at 30iterations 2.3654988E-04 2.8003693E-02 at 40iterations 4.3000065E-05 6.1912537E-03 at 50iterations finished qdiffx linear iterations at : 14:01:47 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 4.3000065E-05 6.1912537E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 14:01:48 4.557u 0.387s 0:05.74 85.8% 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 Mon Oct 10 2011 at 14:01:48 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.918792 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): -11.86200 43.68800 ymin,ymax (A): -22.52500 22.34200 zmin,zma (A): -6.900000 48.76000 x,y,z range (A): 55.55000 44.86700 55.66000 scale (grids/A): 1.918792 object centre (A): 15.91300 -9.1500282E-02 20.93000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 455.2846 centred at (gu) : 86.22260 89.07125 93.38708 assigned negative charge : -455.2713 centred at (gu) : 86.15844 88.78133 93.14674 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24061 grid for indexing accessible points = 1.400000 m= 32545 mr = 64859 m= 4991 mr = 24416 m= 268 mr = 3018 m= 7 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.7100000 number of dielectric boundary points 34675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22719 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) : 0.6395975 object centre at (A) : 15.91300 -9.1500282E-02 20.93000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4130066E-02 1.9150972E-02 midg,1,midg; midg,igrid,midg -4.5918557E-03 1.5430150E-02 1,midg,midg; igrid,midg,midg -3.1268023E-02 1.5991891E-02 gauss-seidel spectral radius is 0.9986873 estimated iterations to convergence 219 setup time was (sec) 1.030000 now iterating at: 14:01:50 rms-change max change #iterations 4.774388 177.3326 at 10iterations 2.277561 68.73331 at 20iterations 1.082747 31.43685 at 30iterations 0.5157544 14.24991 at 40iterations 0.2455698 7.173250 at 50iterations 0.1169255 3.286005 at 60iterations 5.5772081E-02 1.882229 at 70iterations 2.6498990E-02 0.7194715 at 80iterations 1.2702863E-02 0.4072094 at 90iterations 6.0369074E-03 0.1927109 at 100iterations 2.8918590E-03 8.3756447E-02 at 110iterations 1.3827299E-03 4.0550232E-02 at 120iterations finished qdiffx linear iterations at : 14:02:00 total time elapsed so far: 10.92000 # loops : 120 mean,max change (kT/e) : 1.3827299E-03 4.0550232E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 14:02:01 11.082u 0.442s 0:12.34 93.3% 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 14:02:01 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.878189 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): -11.86200 43.68800 ymin,ymax (A): -22.52500 22.34200 zmin,zma (A): -6.900000 48.76000 x,y,z range (A): 55.55000 44.86700 55.66000 scale (grids/A): 2.878189 object centre (A): 15.91300 -9.1500282E-02 20.93000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 1.4008060E-02 assigned positive charge : 455.2846 centred at (gu) : 84.33392 88.60683 95.08035 assigned negative charge : -455.2713 centred at (gu) : 84.23762 88.17208 94.71984 start vw surface at 0.1200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 207099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24061 grid for indexing accessible points = 1.400000 m= 106693 mr = 156683 m= 37663 mr = 88984 m= 8866 mr = 30355 m= 1274 mr = 6499 m= 50 mr = 811 m= 0 mr = 2 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 858 time to turn everything in is 1.870000 number of dielectric boundary points 78311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 23068 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) : 1.918792 object centre at (A) : 15.91300 -9.1500282E-02 20.93000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8055648E-02 0.2772272 midg,1,midg; midg,igrid,midg -3.6684737E-02 0.1703784 1,midg,midg; igrid,midg,midg -0.4161456 0.2718253 gauss-seidel spectral radius is 0.9992748 estimated iterations to convergence 293 setup time was (sec) 2.210000 now iterating at: 14:02:04 rms-change max change #iterations 11.03284 430.3278 at 10iterations 6.494982 140.8661 at 20iterations 3.785843 84.21956 at 30iterations 2.206485 46.60283 at 40iterations 1.282465 22.73859 at 50iterations 0.7460433 14.64858 at 60iterations 0.4325060 8.135103 at 70iterations 0.2512374 4.429843 at 80iterations 0.1456054 2.510080 at 90iterations 8.4356681E-02 1.562874 at 100iterations 4.8937097E-02 0.8286591 at 110iterations 2.8347723E-02 0.4796511 at 120iterations 1.6437653E-02 0.2557163 at 130iterations 9.5385462E-03 0.1590271 at 140iterations 5.5313786E-03 9.2164993E-02 at 150iterations 3.2220776E-03 5.2021027E-02 at 160iterations 1.8887040E-03 3.2735825E-02 at 170iterations 1.1127919E-03 1.8908978E-02 at 180iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 18.86000 # loops : 180 mean,max change (kT/e) : 1.1127919E-03 1.8908978E-02 energy calculations done at 18.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.02000 DelPhi exited at 14:02:22 19.027u 0.485s 0:20.66 94.3% 0+0k 0+0io 0pf+0w