Sat Oct 8 21:07:05 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 21:07:05 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 636 has a net charge of 1.4000 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: 0.6200578 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): -31.44300 17.26700 ymin,ymax (A): -23.58900 22.60500 zmin,zma (A): -12.49200 44.92200 x,y,z range (A): 48.71000 46.19400 57.41400 scale (grids/A): 0.6200578 object centre (A): -7.088000 -0.4919996 16.21500 number of atom coordinates read : 2584 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 88.54814 89.22457 89.59679 assigned negative charge : -390.4956 centred at (gu) : 88.43048 89.28153 89.48219 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6428 nv = 96 ne = 84 npr = 53602 no. pairs analyzed = 53602 no. exposed pairs = 3055 no. arc points = 21793 no. surface atoms = 1012 nbur = 1572 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3521 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.1900000 number of dielectric boundary points 3179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3920023E-09 1.0353935E-08 midg,1,midg; midg,igrid,midg 8.9403693E-09 -2.9731689E-11 1,midg,midg; igrid,midg,midg -5.9293304E-09 8.3801446E-09 gauss-seidel spectral radius is 0.9865255 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 21:07:05 rms-change max change #iterations 0.1315320 22.53606 at 10iterations 1.1706460E-02 1.979713 at 20iterations 1.0908946E-03 0.1950836 at 30iterations 1.0119110E-04 1.5018463E-02 at 40iterations 9.2433202E-06 1.3351440E-03 at 50iterations finished qdiffx linear iterations at : 21:07:08 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 9.2433202E-06 1.3351440E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 21:07:09 3.521u 0.191s 0:04.06 91.3% 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 21:07:09 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 636 has a net charge of 1.4000 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: 1.860173 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): -31.44300 17.26700 ymin,ymax (A): -23.58900 22.60500 zmin,zma (A): -12.49200 44.92200 x,y,z range (A): 48.71000 46.19400 57.41400 scale (grids/A): 1.860173 object centre (A): -7.088000 -0.4919996 16.21500 number of atom coordinates read : 2584 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 85.64375 87.67309 88.79002 assigned negative charge : -390.4956 centred at (gu) : 85.29141 87.84441 88.44630 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21793 grid for indexing accessible points = 1.400000 m= 23701 mr = 49042 m= 3106 mr = 17186 m= 136 mr = 1763 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4655 time to turn everything in is 0.3400000 number of dielectric boundary points 29404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19347 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) : 0.6200578 object centre at (A) : -7.088000 -0.4919996 16.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3287838E-02 2.0056678E-02 midg,1,midg; midg,igrid,midg 1.3242642E-02 1.9809096E-03 1,midg,midg; igrid,midg,midg -3.2207856E-03 4.0336203E-02 gauss-seidel spectral radius is 0.9985662 estimated iterations to convergence 209 setup time was (sec) 0.5700000 now iterating at: 21:07:09 rms-change max change #iterations 4.059334 169.3801 at 10iterations 1.861182 61.56493 at 20iterations 0.8522848 30.17247 at 30iterations 0.3927621 12.77923 at 40iterations 0.1802950 6.563703 at 50iterations 8.2904816E-02 2.827522 at 60iterations 3.8227856E-02 1.445982 at 70iterations 1.7559027E-02 0.5843239 at 80iterations 8.0533233E-03 0.2684860 at 90iterations 3.7111095E-03 0.1369991 at 100iterations 1.7054708E-03 5.3573608E-02 at 110iterations 7.8483240E-04 2.6630402E-02 at 120iterations finished qdiffx linear iterations at : 21:07:17 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 7.8483240E-04 2.6630402E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 21:07:17 8.161u 0.234s 0:08.66 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 21:07:17 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 636 has a net charge of 1.4000 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: 2.790260 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): -31.44300 17.26700 ymin,ymax (A): -23.58900 22.60500 zmin,zma (A): -12.49200 44.92200 x,y,z range (A): 48.71000 46.19400 57.41400 scale (grids/A): 2.790260 object centre (A): -7.088000 -0.4919996 16.21500 number of atom coordinates read : 2584 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 83.46551 86.50960 88.18497 assigned negative charge : -390.4956 centred at (gu) : 82.93707 86.76667 87.66936 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21793 grid for indexing accessible points = 1.400000 m= 79278 mr = 118934 m= 25779 mr = 64737 m= 5277 mr = 20302 m= 565 mr = 3683 m= 21 mr = 330 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 15539 time to turn everything in is 0.8700000 number of dielectric boundary points 66275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19723 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) : 1.860173 object centre at (A) : -7.088000 -0.4919996 16.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2342436 0.2307405 midg,1,midg; midg,igrid,midg 0.1519295 1.1740396E-02 1,midg,midg; igrid,midg,midg -3.6255330E-02 0.5346451 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.120000 now iterating at: 21:07:19 rms-change max change #iterations 9.539334 336.7101 at 10iterations 5.458387 130.1283 at 20iterations 3.113462 62.44880 at 30iterations 1.775567 33.49454 at 40iterations 1.010397 24.30493 at 50iterations 0.5746608 11.71982 at 60iterations 0.3278134 6.245558 at 70iterations 0.1860390 3.521048 at 80iterations 0.1059969 1.887102 at 90iterations 6.0201637E-02 1.141863 at 100iterations 3.4194641E-02 0.6315556 at 110iterations 1.9456863E-02 0.4071808 at 120iterations 1.1063366E-02 0.2113743 at 130iterations 6.2784613E-03 0.1186619 at 140iterations 3.5672232E-03 6.5662384E-02 at 150iterations 2.0347026E-03 3.9295197E-02 at 160iterations 1.1577640E-03 2.0454407E-02 at 170iterations 6.5688527E-04 1.2376785E-02 at 180iterations finished qdiffx linear iterations at : 21:07:31 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 6.5688527E-04 1.2376785E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 21:07:31 13.258u 0.238s 0:13.80 97.6% 0+0k 0+0io 0pf+0w