Tue Oct 11 08:06:03 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 Tue Oct 11 2011 at 08:06:03 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 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: 0.5494336 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): -21.05500 43.01100 ymin,ymax (A): -1.735000 63.05900 zmin,zma (A): 7.173000 54.72100 x,y,z range (A): 64.06600 64.79400 47.54800 scale (grids/A): 0.5494336 object centre (A): 10.97800 30.66200 30.94700 number of atom coordinates read : 3012 total number of charged atoms : 2867 net assigned charge : 8.500025 assigned positive charge : 447.7079 centred at (gu) : 89.89193 90.60265 89.91061 assigned negative charge : -439.2091 centred at (gu) : 89.76358 90.64262 89.92302 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6201 nv = 96 ne = 84 npr = 56652 no. pairs analyzed = 56652 no. exposed pairs = 4308 no. arc points = 31054 no. surface atoms = 1438 nbur = 1574 mkacc time = 0.1200000 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= 229 mr = 2863 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3150 ## 422 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1713735E-10 5.0569465E-10 midg,1,midg; midg,igrid,midg 7.8348150E-10 3.5493000E-10 1,midg,midg; igrid,midg,midg -3.7554412E-10 1.5118988E-09 gauss-seidel spectral radius is 0.9829413 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 08:06:04 rms-change max change #iterations 7.4727207E-02 14.43087 at 10iterations 4.9621980E-03 0.9037285 at 20iterations 3.2839520E-04 4.9324036E-02 at 30iterations 2.3334675E-05 3.7574768E-03 at 40iterations 1.7656399E-06 2.7465820E-04 at 50iterations finished qdiffx linear iterations at : 08:06:06 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.7656399E-06 2.7465820E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:06:07 3.417u 0.207s 0:04.21 85.7% 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 Tue Oct 11 2011 at 08:06:07 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 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: 1.648301 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): -21.05500 43.01100 ymin,ymax (A): -1.735000 63.05900 zmin,zma (A): 7.173000 54.72100 x,y,z range (A): 64.06600 64.79400 47.54800 scale (grids/A): 1.648301 object centre (A): 10.97800 30.66200 30.94700 number of atom coordinates read : 3012 total number of charged atoms : 2867 net assigned charge : 8.500025 assigned positive charge : 447.7079 centred at (gu) : 89.67484 91.80712 89.73064 assigned negative charge : -439.2091 centred at (gu) : 89.29010 91.92747 89.76875 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31054 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19376 mr = 42859 m= 1911 mr = 12386 m= 51 mr = 830 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 80 time to turn everything in is 0.4800000 number of dielectric boundary points 33173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 22006 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) : 0.5494336 object centre at (A) : 10.97800 30.66200 30.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0256436E-03 8.6954217E-03 midg,1,midg; midg,igrid,midg -6.8224533E-03 -1.6395245E-02 1,midg,midg; igrid,midg,midg 9.4912807E-03 2.9955357E-02 gauss-seidel spectral radius is 0.9982445 estimated iterations to convergence 190 setup time was (sec) 0.7900000 now iterating at: 08:06:08 rms-change max change #iterations 3.402286 198.6772 at 10iterations 1.424814 82.09637 at 20iterations 0.5989851 30.74281 at 30iterations 0.2513379 9.603920 at 40iterations 0.1065597 3.937532 at 50iterations 4.4880148E-02 1.584429 at 60iterations 1.8869946E-02 0.6405792 at 70iterations 7.9947878E-03 0.2976494 at 80iterations 3.3652869E-03 0.1230679 at 90iterations 1.4212981E-03 5.0585747E-02 at 100iterations 5.9954688E-04 2.0923615E-02 at 110iterations 2.5310559E-04 1.0238647E-02 at 120iterations finished qdiffx linear iterations at : 08:06:15 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 2.5310559E-04 1.0238647E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:06:16 7.616u 0.244s 0:08.43 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 Tue Oct 11 2011 at 08:06:16 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 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: 2.472451 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): -21.05500 43.01100 ymin,ymax (A): -1.735000 63.05900 zmin,zma (A): 7.173000 54.72100 x,y,z range (A): 64.06600 64.79400 47.54800 scale (grids/A): 2.472451 object centre (A): 10.97800 30.66200 30.94700 number of atom coordinates read : 3012 total number of charged atoms : 2867 net assigned charge : 8.500025 assigned positive charge : 447.7079 centred at (gu) : 89.51205 92.71033 89.59579 assigned negative charge : -439.2091 centred at (gu) : 88.93506 92.89111 89.65314 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 157717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31054 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67141 mr = 105729 m= 18146 mr = 50999 m= 2745 mr = 12809 m= 212 mr = 1656 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 236 time to turn everything in is 1.140000 number of dielectric boundary points 74700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 22916 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) : 1.648301 object centre at (A) : 10.97800 30.66200 30.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6642320E-02 0.1216501 midg,1,midg; midg,igrid,midg -0.1258989 -0.1406842 1,midg,midg; igrid,midg,midg 0.1491483 0.3946169 gauss-seidel spectral radius is 0.9991691 estimated iterations to convergence 274 setup time was (sec) 1.460000 now iterating at: 08:06:17 rms-change max change #iterations 8.836278 327.0295 at 10iterations 5.052305 133.1219 at 20iterations 2.870335 67.13538 at 30iterations 1.614659 46.02418 at 40iterations 0.9068571 19.39899 at 50iterations 0.5074320 11.01495 at 60iterations 0.2838548 6.231209 at 70iterations 0.1582686 3.281616 at 80iterations 8.8156976E-02 1.854872 at 90iterations 4.9202472E-02 1.178963 at 100iterations 2.7280366E-02 0.6066532 at 110iterations 1.5156604E-02 0.3572688 at 120iterations 8.4237438E-03 0.1771631 at 130iterations 4.6916874E-03 0.1027613 at 140iterations 2.5942731E-03 5.1111221E-02 at 150iterations 1.4397447E-03 2.9291153E-02 at 160iterations 8.0071553E-04 1.5375137E-02 at 170iterations 4.4498412E-04 9.8609924E-03 at 180iterations finished qdiffx linear iterations at : 08:06:30 total time elapsed so far: 14.01000 # loops : 180 mean,max change (kT/e) : 4.4498412E-04 9.8609924E-03 energy calculations done at 14.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.19000 DelPhi exited at 08:06:31 14.189u 0.268s 0:14.85 97.2% 0+0k 0+0io 0pf+0w