Sat Oct 8 16:14:15 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 Sat Oct 8 2011 at 16:14:15 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2403 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 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: 0.6533070 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): -1.913000 46.21600 ymin,ymax (A): -15.90300 29.50300 zmin,zma (A): -18.12300 36.36900 x,y,z range (A): 48.12900 45.40600 54.49200 scale (grids/A): 0.6533070 object centre (A): 22.15150 6.800000 9.123000 number of atom coordinates read : 2403 total number of charged atoms : 2335 net assigned charge : 3.306001 assigned positive charge : 360.4318 centred at (gu) : 90.85286 88.62151 90.38840 assigned negative charge : -357.1267 centred at (gu) : 90.91332 88.72168 90.44431 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 48033 no. pairs analyzed = 48033 no. exposed pairs = 3044 no. arc points = 20797 no. surface atoms = 1035 nbur = 1368 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3903 m= 0 mr = 46 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2052 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8373 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4175037E-08 -1.8910156E-09 midg,1,midg; midg,igrid,midg 2.9504434E-08 -6.3151653E-09 1,midg,midg; igrid,midg,midg 1.3446961E-08 -2.9844027E-09 gauss-seidel spectral radius is 0.9878421 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 16:14:15 rms-change max change #iterations 0.1528619 22.43619 at 10iterations 1.5712341E-02 2.442038 at 20iterations 1.6818775E-03 0.2549019 at 30iterations 1.8543038E-04 2.7904510E-02 at 40iterations 2.4824190E-05 3.3788681E-03 at 50iterations finished qdiffx linear iterations at : 16:14:19 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 2.4824190E-05 3.3788681E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 16:14:19 4.144u 0.267s 0:04.70 93.6% 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 Sat Oct 8 2011 at 16:14:19 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2403 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 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: 1.959921 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): -1.913000 46.21600 ymin,ymax (A): -15.90300 29.50300 zmin,zma (A): -18.12300 36.36900 x,y,z range (A): 48.12900 45.40600 54.49200 scale (grids/A): 1.959921 object centre (A): 22.15150 6.800000 9.123000 number of atom coordinates read : 2403 total number of charged atoms : 2335 net assigned charge : 3.306001 assigned positive charge : 360.4318 centred at (gu) : 92.55760 85.86373 91.16468 assigned negative charge : -357.1267 centred at (gu) : 92.73981 86.16494 91.33274 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20797 grid for indexing accessible points = 1.400000 m= 27374 mr = 53016 m= 4734 mr = 20232 m= 290 mr = 3043 m= 1 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.6700000 number of dielectric boundary points 31494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18447 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) : 0.6533070 object centre at (A) : 22.15150 6.800000 9.123000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3163775E-02 -1.2611022E-02 midg,1,midg; midg,igrid,midg 2.6165722E-02 -4.5863311E-03 1,midg,midg; igrid,midg,midg 9.1764135E-03 -4.6753008E-02 gauss-seidel spectral radius is 0.9986896 estimated iterations to convergence 219 setup time was (sec) 0.9800000 now iterating at: 16:14:21 rms-change max change #iterations 4.327617 194.2721 at 10iterations 2.058051 71.98557 at 20iterations 0.9740962 32.68778 at 30iterations 0.4645748 14.69962 at 40iterations 0.2206050 6.731340 at 50iterations 0.1054078 3.286698 at 60iterations 5.0309453E-02 1.629768 at 70iterations 2.3908786E-02 0.7728119 at 80iterations 1.1381764E-02 0.3681717 at 90iterations 5.4127825E-03 0.1712589 at 100iterations 2.5852937E-03 9.3010902E-02 at 110iterations 1.2313970E-03 4.0222168E-02 at 120iterations finished qdiffx linear iterations at : 16:14:29 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 1.2313970E-03 4.0222168E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 16:14:30 9.653u 0.307s 0:10.27 96.8% 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 Sat Oct 8 2011 at 16:14:30 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2403 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 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: 2.939881 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): -1.913000 46.21600 ymin,ymax (A): -15.90300 29.50300 zmin,zma (A): -18.12300 36.36900 x,y,z range (A): 48.12900 45.40600 54.49200 scale (grids/A): 2.939881 object centre (A): 22.15150 6.800000 9.123000 number of atom coordinates read : 2403 total number of charged atoms : 2335 net assigned charge : 3.306001 assigned positive charge : 360.4318 centred at (gu) : 93.83649 83.79555 91.74680 assigned negative charge : -357.1267 centred at (gu) : 94.10962 84.24747 91.99912 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 174798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20797 grid for indexing accessible points = 1.400000 m= 87936 mr = 128403 m= 32772 mr = 72064 m= 8721 mr = 26457 m= 1287 mr = 6645 m= 88 mr = 896 m= 0 mr = 34 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1017 time to turn everything in is 1.740000 number of dielectric boundary points 71103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 18679 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) : 1.959921 object centre at (A) : 22.15150 6.800000 9.123000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2197874 -0.2294775 midg,1,midg; midg,igrid,midg 0.1896329 -6.8378866E-02 1,midg,midg; igrid,midg,midg 8.6247079E-02 -0.6257560 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.070000 now iterating at: 16:14:32 rms-change max change #iterations 10.04477 504.9417 at 10iterations 5.896475 146.3415 at 20iterations 3.451334 72.95868 at 30iterations 2.019616 43.78766 at 40iterations 1.176563 22.63206 at 50iterations 0.6858132 12.85228 at 60iterations 0.3987071 7.254203 at 70iterations 0.2311633 4.717842 at 80iterations 0.1343130 2.503131 at 90iterations 7.7528365E-02 1.393248 at 100iterations 4.4953227E-02 0.8379192 at 110iterations 2.6030120E-02 0.4640627 at 120iterations 1.5077100E-02 0.2587328 at 130iterations 8.7067224E-03 0.1540899 at 140iterations 5.0271126E-03 9.0961456E-02 at 150iterations 2.9124476E-03 5.0022125E-02 at 160iterations 1.6813612E-03 3.1240463E-02 at 170iterations 9.7425969E-04 1.8882751E-02 at 180iterations finished qdiffx linear iterations at : 16:14:46 total time elapsed so far: 16.14000 # loops : 180 mean,max change (kT/e) : 9.7425969E-04 1.8882751E-02 energy calculations done at 16.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.31000 DelPhi exited at 16:14:47 16.316u 0.344s 0:16.94 98.2% 0+0k 0+0io 0pf+0w