Sat Oct 8 17:26:18 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 17:26:18 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 !!! WARNING: ILE 378 has a net charge of -0.2720 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: 0.5479199 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): 37.65700 93.84400 ymin,ymax (A): 16.10300 81.07600 zmin,zma (A): -23.39600 25.12400 x,y,z range (A): 56.18700 64.97301 48.52000 scale (grids/A): 0.5479199 object centre (A): 65.75050 48.58950 0.8640003 number of atom coordinates read : 3348 total number of charged atoms : 3203 net assigned charge : -6.771975 assigned positive charge : 499.5836 centred at (gu) : 90.53342 90.37048 89.96212 assigned negative charge : -506.3568 centred at (gu) : 90.56606 90.31015 89.93775 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6547 nv = 96 ne = 84 npr = 67469 no. pairs analyzed = 67469 no. exposed pairs = 4330 no. arc points = 29163 no. surface atoms = 1465 nbur = 1883 mkacc time = 0.1100000 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= 275 mr = 3430 m= 0 mr = 20 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2300000 number of dielectric boundary points 3372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2997 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8572 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6015682E-10 -2.5514255E-10 midg,1,midg; midg,igrid,midg -8.6762364E-10 3.7628230E-11 1,midg,midg; igrid,midg,midg -1.6915712E-10 -8.2255291E-10 gauss-seidel spectral radius is 0.9828534 estimated iterations to convergence 63 setup time was (sec) 0.4400000 now iterating at: 17:26:19 rms-change max change #iterations 7.8819804E-02 13.73602 at 10iterations 5.4076249E-03 0.8935604 at 20iterations 3.7439202E-04 5.9196472E-02 at 30iterations 4.1403848E-05 8.0575943E-03 at 40iterations 1.0827755E-05 2.2037029E-03 at 50iterations finished qdiffx linear iterations at : 17:26:22 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.0827755E-05 2.2037029E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 17:26:22 3.554u 0.183s 0:04.04 92.3% 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 17:26:22 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 !!! WARNING: ILE 378 has a net charge of -0.2720 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: 1.643759 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): 37.65700 93.84400 ymin,ymax (A): 16.10300 81.07600 zmin,zma (A): -23.39600 25.12400 x,y,z range (A): 56.18700 64.97301 48.52000 scale (grids/A): 1.643759 object centre (A): 65.75050 48.58950 0.8640003 number of atom coordinates read : 3348 total number of charged atoms : 3203 net assigned charge : -6.771975 assigned positive charge : 499.5836 centred at (gu) : 91.59953 91.11066 89.88563 assigned negative charge : -506.3568 centred at (gu) : 91.69775 90.93011 89.81266 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29163 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23767 mr = 49667 m= 2789 mr = 16480 m= 100 mr = 1416 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 558 time to turn everything in is 0.3800000 number of dielectric boundary points 31310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 347 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 24591 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) : 0.5479199 object centre at (A) : 65.75050 48.58950 0.8640003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5974736E-03 -3.7992676E-03 midg,1,midg; midg,igrid,midg -1.0109906E-02 1.6510542E-02 1,midg,midg; igrid,midg,midg -1.2634134E-02 -7.7441959E-03 gauss-seidel spectral radius is 0.9982491 estimated iterations to convergence 190 setup time was (sec) 0.6100000 now iterating at: 17:26:23 rms-change max change #iterations 3.586195 153.4205 at 10iterations 1.513319 55.20813 at 20iterations 0.6426346 23.91491 at 30iterations 0.2719921 12.70020 at 40iterations 0.1151994 3.828468 at 50iterations 4.8869431E-02 1.654570 at 60iterations 2.0669388E-02 0.6891670 at 70iterations 8.8247713E-03 0.2890528 at 80iterations 3.7303867E-03 0.1277504 at 90iterations 1.5933993E-03 5.6613922E-02 at 100iterations 6.8606087E-04 2.5318146E-02 at 110iterations 3.0045360E-04 1.0452271E-02 at 120iterations finished qdiffx linear iterations at : 17:26:31 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 3.0045360E-04 1.0452271E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 17:26:31 8.208u 0.215s 0:08.70 96.6% 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 17:26:31 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 !!! WARNING: ILE 378 has a net charge of -0.2720 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: 2.465639 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): 37.65700 93.84400 ymin,ymax (A): 16.10300 81.07600 zmin,zma (A): -23.39600 25.12400 x,y,z range (A): 56.18700 64.97301 48.52000 scale (grids/A): 2.465639 object centre (A): 65.75050 48.58950 0.8640003 number of atom coordinates read : 3348 total number of charged atoms : 3203 net assigned charge : -6.771975 assigned positive charge : 499.5836 centred at (gu) : 92.39912 91.66596 89.82835 assigned negative charge : -506.3568 centred at (gu) : 92.54642 91.39508 89.71891 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 167798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29163 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 80796 mr = 121574 m= 24299 mr = 64101 m= 4577 mr = 18240 m= 394 mr = 3043 m= 6 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 0.9000000 number of dielectric boundary points 70738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 25590 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) : 1.643759 object centre at (A) : 65.75050 48.58950 0.8640003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2778456E-02 -3.7149925E-02 midg,1,midg; midg,igrid,midg -0.1377933 0.5298197 1,midg,midg; igrid,midg,midg -0.2018427 -6.1590895E-02 gauss-seidel spectral radius is 0.9991661 estimated iterations to convergence 273 setup time was (sec) 1.170000 now iterating at: 17:26:33 rms-change max change #iterations 9.278630 331.3576 at 10iterations 5.257631 128.0407 at 20iterations 2.961243 64.98779 at 30iterations 1.666763 37.40247 at 40iterations 0.9348394 20.45447 at 50iterations 0.5222302 12.37001 at 60iterations 0.2909659 5.775653 at 70iterations 0.1622899 3.273869 at 80iterations 9.0304427E-02 1.792643 at 90iterations 5.0378136E-02 1.014977 at 100iterations 2.7960153E-02 0.5832882 at 110iterations 1.5560618E-02 0.3011322 at 120iterations 8.6501678E-03 0.1768265 at 130iterations 4.8179938E-03 8.9769363E-02 at 140iterations 2.6790276E-03 5.8857918E-02 at 150iterations 1.4927638E-03 2.9336929E-02 at 160iterations 8.3660620E-04 1.7554283E-02 at 170iterations 4.7005032E-04 9.6991062E-03 at 180iterations finished qdiffx linear iterations at : 17:26:45 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 4.7005032E-04 9.6991062E-03 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 17:26:45 13.289u 0.227s 0:13.83 97.6% 0+0k 0+0io 0pf+0w