Sun Oct 9 14:33:39 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 14:33:39 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 = 2771 !!! WARNING: HIQ 137 has a net charge of 0.5140 !!! WARNING: SEP 288 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6548692 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): 20.77400 68.49100 ymin,ymax (A): -25.73700 27.22000 zmin,zma (A): -13.41200 40.95000 x,y,z range (A): 47.71700 52.95700 54.36200 scale (grids/A): 0.6548692 object centre (A): 44.63250 0.7414999 13.76900 number of atom coordinates read : 2771 total number of charged atoms : 2630 net assigned charge : 4.539006 assigned positive charge : 424.6605 centred at (gu) : 89.76653 90.44217 89.97532 assigned negative charge : -420.1224 centred at (gu) : 89.63060 90.38264 89.84463 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7694 nv = 96 ne = 84 npr = 57347 no. pairs analyzed = 57347 no. exposed pairs = 3436 no. arc points = 23642 no. surface atoms = 1154 nbur = 1617 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4134 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2000000 number of dielectric boundary points 3939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2285 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9315 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4862450E-08 3.4102658E-08 midg,1,midg; midg,igrid,midg -9.9846043E-10 2.3243151E-08 1,midg,midg; igrid,midg,midg -1.6632020E-08 3.3547980E-08 gauss-seidel spectral radius is 0.9879254 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 14:33:40 rms-change max change #iterations 0.1681219 26.34418 at 10iterations 1.7795930E-02 2.477016 at 20iterations 1.8370699E-03 0.2811356 at 30iterations 1.9590580E-04 2.6491165E-02 at 40iterations 2.0500909E-05 2.4862289E-03 at 50iterations finished qdiffx linear iterations at : 14:33:43 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.0500909E-05 2.4862289E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:33:43 3.370u 0.177s 0:03.82 92.6% 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 Sun Oct 9 2011 at 14:33:43 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 = 2771 !!! WARNING: HIQ 137 has a net charge of 0.5140 !!! WARNING: SEP 288 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.964608 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): 20.77400 68.49100 ymin,ymax (A): -25.73700 27.22000 zmin,zma (A): -13.41200 40.95000 x,y,z range (A): 47.71700 52.95700 54.36200 scale (grids/A): 1.964608 object centre (A): 44.63250 0.7414999 13.76900 number of atom coordinates read : 2771 total number of charged atoms : 2630 net assigned charge : 4.539006 assigned positive charge : 424.6605 centred at (gu) : 89.29852 91.32590 89.92539 assigned negative charge : -420.1224 centred at (gu) : 88.89163 91.14768 89.53371 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23642 grid for indexing accessible points = 1.400000 m= 28885 mr = 56383 m= 4853 mr = 20583 m= 374 mr = 2907 m= 9 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 36218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20776 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) : 0.6548692 object centre at (A) : 44.63250 0.7414999 13.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3439280E-02 1.8715324E-02 midg,1,midg; midg,igrid,midg 1.0831108E-02 2.7320713E-02 1,midg,midg; igrid,midg,midg 3.8532512E-03 2.9401338E-02 gauss-seidel spectral radius is 0.9987292 estimated iterations to convergence 222 setup time was (sec) 0.6200000 now iterating at: 14:33:44 rms-change max change #iterations 4.746512 216.6207 at 10iterations 2.276448 75.49895 at 20iterations 1.095271 33.68406 at 30iterations 0.5275983 16.68474 at 40iterations 0.2530062 7.872028 at 50iterations 0.1218550 3.467595 at 60iterations 5.8424901E-02 1.762597 at 70iterations 2.8216479E-02 0.8157063 at 80iterations 1.3568179E-02 0.4189224 at 90iterations 6.5438631E-03 0.2121334 at 100iterations 3.1237300E-03 9.4485760E-02 at 110iterations 1.5128594E-03 4.3346405E-02 at 120iterations finished qdiffx linear iterations at : 14:33:51 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.5128594E-03 4.3346405E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 14:33:51 7.830u 0.202s 0:08.34 96.2% 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 Sun Oct 9 2011 at 14:33:52 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 = 2771 !!! WARNING: HIQ 137 has a net charge of 0.5140 !!! WARNING: SEP 288 has a net charge of -0.4750 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: 2.946912 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): 20.77400 68.49100 ymin,ymax (A): -25.73700 27.22000 zmin,zma (A): -13.41200 40.95000 x,y,z range (A): 47.71700 52.95700 54.36200 scale (grids/A): 2.946912 object centre (A): 44.63250 0.7414999 13.76900 number of atom coordinates read : 2771 total number of charged atoms : 2630 net assigned charge : 4.539006 assigned positive charge : 424.6605 centred at (gu) : 88.94777 91.98879 89.88791 assigned negative charge : -420.1224 centred at (gu) : 88.33739 91.72155 89.30038 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 189739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23642 grid for indexing accessible points = 1.400000 m= 93822 mr = 137038 m= 33697 mr = 75204 m= 8834 mr = 26342 m= 1412 mr = 6434 m= 128 mr = 899 m= 5 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 81669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21031 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) : 1.964608 object centre at (A) : 44.63250 0.7414999 13.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8367309 0.1134369 midg,1,midg; midg,igrid,midg 3.7992711E-03 0.2871394 1,midg,midg; igrid,midg,midg 4.3941967E-02 0.1912291 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.300000 now iterating at: 14:33:53 rms-change max change #iterations 11.00998 396.1354 at 10iterations 6.517037 163.4453 at 20iterations 3.844205 83.10258 at 30iterations 2.257965 44.36195 at 40iterations 1.324535 25.96869 at 50iterations 0.7759857 13.35499 at 60iterations 0.4523003 8.131311 at 70iterations 0.2634188 4.805315 at 80iterations 0.1539858 2.703711 at 90iterations 8.9706033E-02 1.491798 at 100iterations 5.2183989E-02 0.9896927 at 110iterations 3.0338209E-02 0.5180206 at 120iterations 1.7635351E-02 0.3166914 at 130iterations 1.0248141E-02 0.1859627 at 140iterations 5.9581660E-03 0.1141434 at 150iterations 3.4591195E-03 6.1721802E-02 at 160iterations 2.0128300E-03 3.3435822E-02 at 170iterations 1.1741809E-03 1.8884659E-02 at 180iterations finished qdiffx linear iterations at : 14:34:05 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 1.1741809E-03 1.8884659E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 14:34:05 13.104u 0.198s 0:13.58 97.8% 0+0k 0+0io 0pf+0w