Mon Oct 10 17:05:10 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 17:05:10 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 = 2503 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: 0.5560588 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): -6.619000 40.77300 ymin,ymax (A): -9.551001 42.11500 zmin,zma (A): -1.484000 62.53800 x,y,z range (A): 47.39200 51.66600 64.02200 scale (grids/A): 0.5560588 object centre (A): 17.07700 16.28200 30.52700 number of atom coordinates read : 2503 total number of charged atoms : 2366 net assigned charge : 7.000025 assigned positive charge : 368.0840 centred at (gu) : 90.33103 88.97047 89.43179 assigned negative charge : -361.0848 centred at (gu) : 90.37148 88.88558 89.55988 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5067 nv = 96 ne = 84 npr = 50345 no. pairs analyzed = 50345 no. exposed pairs = 3211 no. arc points = 23133 no. surface atoms = 1077 nbur = 1426 mkacc time = 0.1300000 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 = 1.540000 m= 199 mr = 2551 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2379 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6608 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8711899E-09 -3.1862932E-10 midg,1,midg; midg,igrid,midg -4.2267301E-11 1.0155853E-09 1,midg,midg; igrid,midg,midg 8.8606017E-10 3.5289210E-10 gauss-seidel spectral radius is 0.9832848 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 17:05:11 rms-change max change #iterations 7.2774626E-02 13.77158 at 10iterations 5.0221598E-03 0.8515186 at 20iterations 3.4930606E-04 6.1292648E-02 at 30iterations 2.5066702E-05 4.4937134E-03 at 40iterations 1.7845425E-06 3.5095215E-04 at 50iterations finished qdiffx linear iterations at : 17:05:16 total time elapsed so far: 5.110000 # loops : 50 mean,max change (kT/e) : 1.7845425E-06 3.5095215E-04 energy calculations done at 5.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 17:05:16 5.293u 0.443s 0:06.24 91.8% 0+0k 0+0io 3pf+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 17:05:16 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 = 2503 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: 1.668177 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): -6.619000 40.77300 ymin,ymax (A): -9.551001 42.11500 zmin,zma (A): -1.484000 62.53800 x,y,z range (A): 47.39200 51.66600 64.02200 scale (grids/A): 1.668177 object centre (A): 17.07700 16.28200 30.52700 number of atom coordinates read : 2503 total number of charged atoms : 2366 net assigned charge : 7.000025 assigned positive charge : 368.0840 centred at (gu) : 90.99255 86.91069 88.29469 assigned negative charge : -361.0848 centred at (gu) : 91.11447 86.65680 88.67957 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 56074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23133 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17251 mr = 37277 m= 1866 mr = 11779 m= 60 mr = 905 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 253 time to turn everything in is 0.5100000 number of dielectric boundary points 25287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18214 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) : 0.5560588 object centre at (A) : 17.07700 16.28200 30.52700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3087397E-02 1.2537407E-02 midg,1,midg; midg,igrid,midg -9.0348162E-03 5.9437985E-03 1,midg,midg; igrid,midg,midg 7.4557210E-03 1.7596519E-03 gauss-seidel spectral radius is 0.9982094 estimated iterations to convergence 188 setup time was (sec) 0.8500000 now iterating at: 17:05:18 rms-change max change #iterations 3.091031 135.8250 at 10iterations 1.295729 54.90767 at 20iterations 0.5403237 19.89218 at 30iterations 0.2263041 8.581786 at 40iterations 9.5090076E-02 3.574335 at 50iterations 3.9836414E-02 1.525271 at 60iterations 1.6732326E-02 0.6279559 at 70iterations 6.9971634E-03 0.2935276 at 80iterations 2.9212071E-03 0.1099873 at 90iterations 1.2244722E-03 4.8656464E-02 at 100iterations 5.1481760E-04 1.8218994E-02 at 110iterations 2.1546932E-04 8.6724758E-03 at 120iterations finished qdiffx linear iterations at : 17:05:29 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 2.1546932E-04 8.6724758E-03 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 17:05:30 12.027u 0.485s 0:13.55 92.2% 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 17:05:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.502265 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): -6.619000 40.77300 ymin,ymax (A): -9.551001 42.11500 zmin,zma (A): -1.484000 62.53800 x,y,z range (A): 47.39200 51.66600 64.02200 scale (grids/A): 2.502265 object centre (A): 17.07700 16.28200 30.52700 number of atom coordinates read : 2503 total number of charged atoms : 2366 net assigned charge : 7.000025 assigned positive charge : 368.0840 centred at (gu) : 91.48866 85.36593 87.44183 assigned negative charge : -361.0848 centred at (gu) : 91.67175 84.98515 88.01927 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 130281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23133 grid for indexing accessible points = 1.400000 m= 59627 mr = 91433 m= 17095 mr = 46862 m= 2907 mr = 12734 m= 237 mr = 1910 m= 7 mr = 112 m= 0 mr = 2 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 784 time to turn everything in is 1.160000 number of dielectric boundary points 57101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 18908 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) : 1.668177 object centre at (A) : 17.07700 16.28200 30.52700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2830569 0.2550693 midg,1,midg; midg,igrid,midg -9.3602076E-02 0.1330759 1,midg,midg; igrid,midg,midg 9.0959333E-02 8.9449808E-03 gauss-seidel spectral radius is 0.9991346 estimated iterations to convergence 269 setup time was (sec) 1.550000 now iterating at: 17:05:32 rms-change max change #iterations 7.928802 251.6010 at 10iterations 4.441681 131.5042 at 20iterations 2.465564 63.28202 at 30iterations 1.364561 33.46984 at 40iterations 0.7524685 17.70082 at 50iterations 0.4152132 9.833964 at 60iterations 0.2286877 5.518255 at 70iterations 0.1255845 2.734276 at 80iterations 6.8846345E-02 1.534237 at 90iterations 3.7873238E-02 0.8096142 at 100iterations 2.0733684E-02 0.4528656 at 110iterations 1.1376951E-02 0.2418690 at 120iterations 6.2373593E-03 0.1352139 at 130iterations 3.4154775E-03 7.8629017E-02 at 140iterations 1.8720842E-03 3.8978577E-02 at 150iterations 1.0264739E-03 2.1638870E-02 at 160iterations 5.6206150E-04 1.4271736E-02 at 170iterations 3.0821969E-04 6.5441132E-03 at 180iterations finished qdiffx linear iterations at : 17:05:50 total time elapsed so far: 19.82000 # loops : 180 mean,max change (kT/e) : 3.0821969E-04 6.5441132E-03 energy calculations done at 19.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.00000 DelPhi exited at 17:05:51 20.003u 0.543s 0:20.98 97.9% 0+0k 0+0io 0pf+0w