Sun Oct 9 16:19:07 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 Sun Oct 9 2011 at 16:19:07 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6227805 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): -20.31200 35.06000 ymin,ymax (A): 54.41100 106.4260 zmin,zma (A): -0.8040000 56.35900 x,y,z range (A): 55.37200 52.01500 57.16300 scale (grids/A): 0.6227805 object centre (A): 7.373999 80.41850 27.77750 number of atom coordinates read : 3024 total number of charged atoms : 2882 net assigned charge : -2.499985 assigned positive charge : 451.0390 centred at (gu) : 90.65811 90.38908 89.90266 assigned negative charge : -453.5403 centred at (gu) : 90.65261 90.27007 90.03504 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7754 nv = 96 ne = 84 npr = 61411 no. pairs analyzed = 61411 no. exposed pairs = 3974 no. arc points = 27617 no. surface atoms = 1330 nbur = 1694 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4006 m= 0 mr = 51 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3200000 number of dielectric boundary points 4104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2750 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9418801E-09 -1.3258491E-08 midg,1,midg; midg,igrid,midg -1.1367566E-08 8.3598195E-09 1,midg,midg; igrid,midg,midg -2.3454270E-09 -2.0351760E-09 gauss-seidel spectral radius is 0.9866884 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 16:19:08 rms-change max change #iterations 0.1376216 21.34690 at 10iterations 1.3040341E-02 1.629749 at 20iterations 1.2816025E-03 0.1879272 at 30iterations 1.7440942E-04 2.0900726E-02 at 40iterations 4.1007694E-05 4.5089722E-03 at 50iterations finished qdiffx linear iterations at : 16:19:11 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 4.1007694E-05 4.5089722E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 16:19:11 3.560u 0.144s 0:03.97 93.1% 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 Sun Oct 9 2011 at 16:19:11 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.868341 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): -20.31200 35.06000 ymin,ymax (A): 54.41100 106.4260 zmin,zma (A): -0.8040000 56.35900 x,y,z range (A): 55.37200 52.01500 57.16300 scale (grids/A): 1.868341 object centre (A): 7.373999 80.41850 27.77750 number of atom coordinates read : 3024 total number of charged atoms : 2882 net assigned charge : -2.499985 assigned positive charge : 451.0390 centred at (gu) : 91.97343 91.16664 89.70745 assigned negative charge : -453.5403 centred at (gu) : 91.95763 90.80983 90.10474 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27617 grid for indexing accessible points = 1.400000 m= 28462 mr = 56496 m= 4346 mr = 19917 m= 241 mr = 2585 m= 0 mr = 74 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 813 time to turn everything in is 0.5800000 number of dielectric boundary points 37807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22616 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) : 0.6227805 object centre at (A) : 7.373999 80.41850 27.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1223584E-02 -1.9655773E-02 midg,1,midg; midg,igrid,midg -1.7725419E-02 -1.9133858E-02 1,midg,midg; igrid,midg,midg -1.1276880E-02 -3.1298462E-02 gauss-seidel spectral radius is 0.9986352 estimated iterations to convergence 215 setup time was (sec) 0.8400000 now iterating at: 16:19:12 rms-change max change #iterations 4.490334 170.4296 at 10iterations 2.087793 71.93747 at 20iterations 0.9799606 29.23788 at 30iterations 0.4592417 13.96836 at 40iterations 0.2143806 6.283756 at 50iterations 0.1006597 3.361725 at 60iterations 4.7267705E-02 1.486014 at 70iterations 2.2129573E-02 0.6520548 at 80iterations 1.0373732E-02 0.3049183 at 90iterations 4.8665609E-03 0.1463900 at 100iterations 2.2867678E-03 7.2782516E-02 at 110iterations 1.0817368E-03 3.5123825E-02 at 120iterations finished qdiffx linear iterations at : 16:19:18 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 1.0817368E-03 3.5123825E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 16:19:19 7.148u 0.156s 0:07.57 96.3% 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 Sun Oct 9 2011 at 16:19:19 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 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: 2.802512 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): -20.31200 35.06000 ymin,ymax (A): 54.41100 106.4260 zmin,zma (A): -0.8040000 56.35900 x,y,z range (A): 55.37200 52.01500 57.16300 scale (grids/A): 2.802512 object centre (A): 7.373999 80.41850 27.77750 number of atom coordinates read : 3024 total number of charged atoms : 2882 net assigned charge : -2.499985 assigned positive charge : 451.0390 centred at (gu) : 92.95996 91.74978 89.56081 assigned negative charge : -453.5403 centred at (gu) : 92.93636 91.21468 90.15708 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 193773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27617 grid for indexing accessible points = 1.400000 m= 92509 mr = 137604 m= 32864 mr = 73084 m= 7792 mr = 25688 m= 986 mr = 5685 m= 50 mr = 631 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2800 time to turn everything in is 1.410000 number of dielectric boundary points 85260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 23048 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) : 1.868341 object centre at (A) : 7.373999 80.41850 27.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8219084 -0.2676413 midg,1,midg; midg,igrid,midg -0.2144646 -0.3910851 1,midg,midg; igrid,midg,midg -0.1481310 -0.4783582 gauss-seidel spectral radius is 0.9992783 estimated iterations to convergence 294 setup time was (sec) 1.670000 now iterating at: 16:19:20 rms-change max change #iterations 10.72231 360.9447 at 10iterations 6.383441 162.2128 at 20iterations 3.779517 83.32396 at 30iterations 2.224110 47.62175 at 40iterations 1.307803 27.92088 at 50iterations 0.7633688 15.72188 at 60iterations 0.4458596 8.446182 at 70iterations 0.2606076 5.125271 at 80iterations 0.1518240 2.805870 at 90iterations 8.8447809E-02 1.769257 at 100iterations 5.1491156E-02 0.9803572 at 110iterations 2.9880518E-02 0.5720978 at 120iterations 1.7347660E-02 0.3122559 at 130iterations 1.0065187E-02 0.1917877 at 140iterations 5.8382973E-03 0.1055489 at 150iterations 3.3877627E-03 6.4655304E-02 at 160iterations 1.9661628E-03 3.5599232E-02 at 170iterations 1.1407564E-03 2.2144318E-02 at 180iterations finished qdiffx linear iterations at : 16:19:30 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 1.1407564E-03 2.2144318E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 16:19:30 11.218u 0.175s 0:11.66 97.5% 0+0k 0+0io 0pf+0w