Sun Oct 9 06:16:18 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 06:16:18 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6636344 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): 1.792000 44.37600 ymin,ymax (A): -9.402000 39.11600 zmin,zma (A): -24.34100 29.30300 x,y,z range (A): 42.58400 48.51800 53.64400 scale (grids/A): 0.6636344 object centre (A): 23.08400 14.85700 2.481000 number of atom coordinates read : 1994 total number of charged atoms : 1851 net assigned charge : -1.593986 assigned positive charge : 301.2799 centred at (gu) : 90.04952 88.93417 88.23289 assigned negative charge : -302.8741 centred at (gu) : 89.88847 88.77866 88.20509 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5920 nv = 96 ne = 84 npr = 41782 no. pairs analyzed = 41782 no. exposed pairs = 2443 no. arc points = 17571 no. surface atoms = 822 nbur = 1172 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3281 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.2600000 number of dielectric boundary points 2959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2569600E-08 3.9462209E-10 midg,1,midg; midg,igrid,midg -3.8400856E-08 1.7371690E-08 1,midg,midg; igrid,midg,midg -3.1296818E-08 2.2921389E-08 gauss-seidel spectral radius is 0.9881759 estimated iterations to convergence 75 setup time was (sec) 0.4800000 now iterating at: 06:16:19 rms-change max change #iterations 0.1544925 25.04076 at 10iterations 1.6875289E-02 2.595709 at 20iterations 1.7805388E-03 0.2838211 at 30iterations 1.8952330E-04 3.1645775E-02 at 40iterations 2.0206380E-05 3.0918121E-03 at 50iterations finished qdiffx linear iterations at : 06:16:21 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.0206380E-05 3.0918121E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 06:16:22 3.088u 0.144s 0:03.51 91.7% 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 Sun Oct 9 2011 at 06:16:22 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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: 1.990903 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): 1.792000 44.37600 ymin,ymax (A): -9.402000 39.11600 zmin,zma (A): -24.34100 29.30300 x,y,z range (A): 42.58400 48.51800 53.64400 scale (grids/A): 1.990903 object centre (A): 23.08400 14.85700 2.481000 number of atom coordinates read : 1994 total number of charged atoms : 1851 net assigned charge : -1.593986 assigned positive charge : 301.2799 centred at (gu) : 90.14843 86.80255 84.69855 assigned negative charge : -302.8741 centred at (gu) : 89.66549 86.33620 84.61562 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17571 grid for indexing accessible points = 1.400000 m= 23411 mr = 43378 m= 4102 mr = 17575 m= 310 mr = 2787 m= 2 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1669 time to turn everything in is 0.4900000 number of dielectric boundary points 27121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14634 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) : 0.6636344 object centre at (A) : 23.08400 14.85700 2.481000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9987762E-02 1.8163042E-02 midg,1,midg; midg,igrid,midg -3.1687602E-02 9.6105356E-03 1,midg,midg; igrid,midg,midg -2.5522375E-02 1.7081596E-02 gauss-seidel spectral radius is 0.9986818 estimated iterations to convergence 218 setup time was (sec) 0.7700000 now iterating at: 06:16:23 rms-change max change #iterations 4.120719 212.2661 at 10iterations 1.947435 67.01939 at 20iterations 0.9227592 32.45934 at 30iterations 0.4383259 15.73728 at 40iterations 0.2073428 6.942277 at 50iterations 9.8586172E-02 3.356379 at 60iterations 4.6734463E-02 1.565950 at 70iterations 2.2143606E-02 0.8134794 at 80iterations 1.0520482E-02 0.3512449 at 90iterations 4.9791136E-03 0.1723610 at 100iterations 2.3599288E-03 7.2593689E-02 at 110iterations 1.1181623E-03 3.7206650E-02 at 120iterations finished qdiffx linear iterations at : 06:16:29 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 1.1181623E-03 3.7206650E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 06:16:30 7.394u 0.232s 0:07.91 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 06:16:30 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.986355 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): 1.792000 44.37600 ymin,ymax (A): -9.402000 39.11600 zmin,zma (A): -24.34100 29.30300 x,y,z range (A): 42.58400 48.51800 53.64400 scale (grids/A): 2.986355 object centre (A): 23.08400 14.85700 2.481000 number of atom coordinates read : 1994 total number of charged atoms : 1851 net assigned charge : -1.593986 assigned positive charge : 301.2799 centred at (gu) : 90.22275 85.20377 82.04782 assigned negative charge : -302.8741 centred at (gu) : 89.49828 84.50428 81.92343 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 145516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17571 grid for indexing accessible points = 1.400000 m= 74938 mr = 104657 m= 28586 mr = 61838 m= 7814 mr = 23504 m= 1392 mr = 6178 m= 107 mr = 1008 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 5549 time to turn everything in is 1.180000 number of dielectric boundary points 61137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 14808 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) : 1.990903 object centre at (A) : 23.08400 14.85700 2.481000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5364529 0.3671684 midg,1,midg; midg,igrid,midg -0.2230048 0.1322143 1,midg,midg; igrid,midg,midg -0.2459140 0.1434108 gauss-seidel spectral radius is 0.9992548 estimated iterations to convergence 289 setup time was (sec) 1.490000 now iterating at: 06:16:31 rms-change max change #iterations 9.398075 342.3678 at 10iterations 5.398309 133.4833 at 20iterations 3.114960 61.32050 at 30iterations 1.788431 39.47472 at 40iterations 1.027676 21.14783 at 50iterations 0.5894212 11.66187 at 60iterations 0.3377747 6.563253 at 70iterations 0.1931526 3.812760 at 80iterations 0.1106965 2.093460 at 90iterations 6.3481241E-02 1.231000 at 100iterations 3.6301218E-02 0.7163906 at 110iterations 2.0779878E-02 0.3893433 at 120iterations 1.1885988E-02 0.2322388 at 130iterations 6.8061156E-03 0.1337128 at 140iterations 3.8993973E-03 7.4622154E-02 at 150iterations 2.2385367E-03 4.2144775E-02 at 160iterations 1.2806453E-03 2.5130749E-02 at 170iterations 7.3264755E-04 1.4181137E-02 at 180iterations finished qdiffx linear iterations at : 06:16:42 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 7.3264755E-04 1.4181137E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 06:16:43 12.433u 0.277s 0:12.98 97.8% 0+0k 0+0io 0pf+0w