Tue Oct 11 06:57:04 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 06:57:04 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 = 3043 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: 0.5489421 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): -20.17400 44.67800 ymin,ymax (A): 19.67600 76.04700 zmin,zma (A): -70.34900 -21.03300 x,y,z range (A): 64.85201 56.37100 49.31600 scale (grids/A): 0.5489421 object centre (A): 12.25200 47.86150 -45.69100 number of atom coordinates read : 3043 total number of charged atoms : 2903 net assigned charge : -0.4999801 assigned positive charge : 447.3434 centred at (gu) : 89.85895 90.01971 90.24313 assigned negative charge : -447.8440 centred at (gu) : 89.83665 90.21988 90.26619 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5899 nv = 96 ne = 84 npr = 63043 no. pairs analyzed = 63043 no. exposed pairs = 3905 no. arc points = 27593 no. surface atoms = 1317 nbur = 1726 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 = 1.568000 m= 244 mr = 2987 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2846 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3148531E-10 -2.1806183E-10 midg,1,midg; midg,igrid,midg 1.4212906E-09 -1.5756720E-09 1,midg,midg; igrid,midg,midg -2.0657186E-10 1.2938725E-10 gauss-seidel spectral radius is 0.9828960 estimated iterations to convergence 63 setup time was (sec) 0.6400000 now iterating at: 06:57:05 rms-change max change #iterations 7.6951161E-02 13.67384 at 10iterations 5.1153819E-03 0.9570045 at 20iterations 3.5237640E-04 5.5641174E-02 at 30iterations 2.3513299E-05 4.2114258E-03 at 40iterations 1.6132215E-06 2.9373169E-04 at 50iterations finished qdiffx linear iterations at : 06:57:08 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 1.6132215E-06 2.9373169E-04 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 06:57:09 4.101u 0.276s 0:04.88 89.5% 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 06:57:09 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 = 3043 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: 1.646827 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): -20.17400 44.67800 ymin,ymax (A): 19.67600 76.04700 zmin,zma (A): -70.34900 -21.03300 x,y,z range (A): 64.85201 56.37100 49.31600 scale (grids/A): 1.646827 object centre (A): 12.25200 47.86150 -45.69100 number of atom coordinates read : 3043 total number of charged atoms : 2903 net assigned charge : -0.4999801 assigned positive charge : 447.3434 centred at (gu) : 89.57645 90.05871 90.72896 assigned negative charge : -447.8440 centred at (gu) : 89.50959 90.65923 90.79826 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 64202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20590 mr = 42598 m= 2302 mr = 14253 m= 54 mr = 1173 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 717 time to turn everything in is 0.6000000 number of dielectric boundary points 29119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 291 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22309 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) : 0.5489421 object centre at (A) : 12.25200 47.86150 -45.69100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2466036E-03 1.3252545E-02 midg,1,midg; midg,igrid,midg 3.9085462E-05 -1.1628552E-02 1,midg,midg; igrid,midg,midg 4.2272341E-03 -3.7625234E-03 gauss-seidel spectral radius is 0.9982282 estimated iterations to convergence 189 setup time was (sec) 0.8900000 now iterating at: 06:57:10 rms-change max change #iterations 3.386419 187.6837 at 10iterations 1.418968 54.91008 at 20iterations 0.5966163 20.76251 at 30iterations 0.2514138 9.902802 at 40iterations 0.1057615 3.885941 at 50iterations 4.4305719E-02 1.644273 at 60iterations 1.8759370E-02 0.7024269 at 70iterations 7.8748940E-03 0.2893937 at 80iterations 3.3240283E-03 0.1116409 at 90iterations 1.3992420E-03 5.3085327E-02 at 100iterations 5.9013761E-04 2.3263931E-02 at 110iterations 2.4883216E-04 8.6555481E-03 at 120iterations finished qdiffx linear iterations at : 06:57:18 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 2.4883216E-04 8.6555481E-03 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 06:57:19 9.271u 0.298s 0:10.00 95.6% 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 06:57:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 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: 2.470240 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): -20.17400 44.67800 ymin,ymax (A): 19.67600 76.04700 zmin,zma (A): -70.34900 -21.03300 x,y,z range (A): 64.85201 56.37100 49.31600 scale (grids/A): 2.470240 object centre (A): 12.25200 47.86150 -45.69100 number of atom coordinates read : 3043 total number of charged atoms : 2903 net assigned charge : -0.4999801 assigned positive charge : 447.3434 centred at (gu) : 89.36456 90.08802 91.09324 assigned negative charge : -447.8440 centred at (gu) : 89.26422 90.98885 91.19719 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 148935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27593 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69101 mr = 104191 m= 21651 mr = 54597 m= 3755 mr = 16553 m= 205 mr = 2485 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 2340 time to turn everything in is 1.450000 number of dielectric boundary points 65747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 23199 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) : 1.646827 object centre at (A) : 12.25200 47.86150 -45.69100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1643933 0.2273012 midg,1,midg; midg,igrid,midg 1.6875705E-03 -0.1435656 1,midg,midg; igrid,midg,midg 4.0096637E-02 3.9896514E-02 gauss-seidel spectral radius is 0.9991539 estimated iterations to convergence 272 setup time was (sec) 1.770000 now iterating at: 06:57:21 rms-change max change #iterations 8.759254 265.4857 at 10iterations 4.913246 118.3831 at 20iterations 2.752990 65.82236 at 30iterations 1.537973 32.37471 at 40iterations 0.8569456 16.74235 at 50iterations 0.4754746 10.21430 at 60iterations 0.2634980 5.783765 at 70iterations 0.1463960 3.198435 at 80iterations 8.0808282E-02 1.827861 at 90iterations 4.4717144E-02 0.8927069 at 100iterations 2.4704041E-02 0.5005732 at 110iterations 1.3687408E-02 0.3027172 at 120iterations 7.5460221E-03 0.1432858 at 130iterations 4.1765636E-03 8.2281888E-02 at 140iterations 2.3045100E-03 4.8948288E-02 at 150iterations 1.2709170E-03 2.5014877E-02 at 160iterations 7.0100237E-04 1.3784409E-02 at 170iterations 3.8745953E-04 7.5588226E-03 at 180iterations finished qdiffx linear iterations at : 06:57:34 total time elapsed so far: 15.13000 # loops : 180 mean,max change (kT/e) : 3.8745953E-04 7.5588226E-03 energy calculations done at 15.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.30000 DelPhi exited at 06:57:35 15.304u 0.319s 0:16.12 96.8% 0+0k 0+0io 0pf+0w