Sat Oct 8 11:38:32 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 11:38:32 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4198 !!! WARNING: HIT 441 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5269624 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): -3.087000 64.47000 ymin,ymax (A): -12.09100 38.47800 zmin,zma (A): -19.53400 45.17100 x,y,z range (A): 67.55700 50.56900 64.70500 scale (grids/A): 0.5269624 object centre (A): 30.69150 13.19350 12.81850 number of atom coordinates read : 4198 total number of charged atoms : 4046 net assigned charge : -4.485950 assigned positive charge : 628.3021 centred at (gu) : 88.60378 90.13428 90.68096 assigned negative charge : -632.7906 centred at (gu) : 88.61947 90.23946 90.67944 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7331 nv = 96 ne = 84 npr = 88486 no. pairs analyzed = 88486 no. exposed pairs = 4835 no. arc points = 32400 no. surface atoms = 1651 nbur = 2547 mkacc time = 0.1500000 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 = 1.596000 m= 265 mr = 4105 m= 0 mr = 19 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3310 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9876 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1488019E-10 -1.4486674E-10 midg,1,midg; midg,igrid,midg 3.2760822E-10 -6.3225619E-10 1,midg,midg; igrid,midg,midg -8.1240605E-11 -1.4108079E-10 gauss-seidel spectral radius is 0.9815281 estimated iterations to convergence 61 setup time was (sec) 0.4900000 now iterating at: 11:38:33 rms-change max change #iterations 7.3301554E-02 11.72976 at 10iterations 5.0342688E-03 0.7672005 at 20iterations 7.2547345E-04 9.2506409E-02 at 30iterations 2.1492862E-04 2.2909641E-02 at 40iterations 6.9890135E-05 7.9343319E-03 at 50iterations finished qdiffx linear iterations at : 11:38:37 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 6.9890135E-05 7.9343319E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 11:38:38 3.791u 0.445s 0:05.91 71.5% 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 11:38:38 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4198 !!! WARNING: HIT 441 has a net charge of 0.5140 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: 1.580887 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): -3.087000 64.47000 ymin,ymax (A): -12.09100 38.47800 zmin,zma (A): -19.53400 45.17100 x,y,z range (A): 67.55700 50.56900 64.70500 scale (grids/A): 1.580887 object centre (A): 30.69150 13.19350 12.81850 number of atom coordinates read : 4198 total number of charged atoms : 4046 net assigned charge : -4.485950 assigned positive charge : 628.3021 centred at (gu) : 85.81044 90.40195 92.04180 assigned negative charge : -632.7906 centred at (gu) : 85.85801 90.71795 92.03782 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32400 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 25708 mr = 60215 m= 2508 mr = 18102 m= 52 mr = 1199 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.4300000 number of dielectric boundary points 32357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 30742 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) : 0.5269624 object centre at (A) : 30.69150 13.19350 12.81850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8294111E-03 -9.0242652E-03 midg,1,midg; midg,igrid,midg 3.2349650E-03 -1.4121799E-02 1,midg,midg; igrid,midg,midg 1.4232892E-02 1.3277235E-02 gauss-seidel spectral radius is 0.9981713 estimated iterations to convergence 186 setup time was (sec) 0.6600000 now iterating at: 11:38:39 rms-change max change #iterations 3.766826 153.3105 at 10iterations 1.568342 50.41737 at 20iterations 0.6538985 22.48465 at 30iterations 0.2726657 8.289698 at 40iterations 0.1138432 3.487086 at 50iterations 4.7552664E-02 1.573842 at 60iterations 1.9901877E-02 0.6108704 at 70iterations 8.4392959E-03 0.2956715 at 80iterations 3.6376060E-03 0.1208172 at 90iterations 1.6419603E-03 4.9958885E-02 at 100iterations 8.0591574E-04 2.3607254E-02 at 110iterations 4.3662373E-04 1.2928963E-02 at 120iterations finished qdiffx linear iterations at : 11:38:50 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 4.3662373E-04 1.2928963E-02 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 11:38:51 8.509u 0.824s 0:12.92 72.1% 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 Sat Oct 8 2011 at 11:38:51 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4198 !!! WARNING: HIT 441 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.371331 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): -3.087000 64.47000 ymin,ymax (A): -12.09100 38.47800 zmin,zma (A): -19.53400 45.17100 x,y,z range (A): 67.55700 50.56900 64.70500 scale (grids/A): 2.371331 object centre (A): 30.69150 13.19350 12.81850 number of atom coordinates read : 4198 total number of charged atoms : 4046 net assigned charge : -4.485950 assigned positive charge : 628.3021 centred at (gu) : 83.71518 90.60263 93.06259 assigned negative charge : -632.7906 centred at (gu) : 83.78684 91.07685 93.05670 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 194937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32400 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 91687 mr = 147106 m= 24822 mr = 74141 m= 3781 mr = 18606 m= 174 mr = 2414 m= 5 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1660 time to turn everything in is 1.040000 number of dielectric boundary points 73097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 32317 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) : 1.580887 object centre at (A) : 30.69150 13.19350 12.81850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2343910 -0.2006562 midg,1,midg; midg,igrid,midg 4.5265626E-02 -0.2130952 1,midg,midg; igrid,midg,midg 0.3820449 0.2914703 gauss-seidel spectral radius is 0.9991569 estimated iterations to convergence 272 setup time was (sec) 1.330000 now iterating at: 11:38:53 rms-change max change #iterations 9.952896 244.7949 at 10iterations 5.660154 137.8550 at 20iterations 3.196884 67.52551 at 30iterations 1.794639 36.28988 at 40iterations 1.002243 20.82287 at 50iterations 0.5609213 10.18829 at 60iterations 0.3124524 5.689997 at 70iterations 0.1737828 3.316877 at 80iterations 9.6778937E-02 1.789105 at 90iterations 5.3678043E-02 1.078247 at 100iterations 2.9854443E-02 0.5520573 at 110iterations 1.6579114E-02 0.3043356 at 120iterations 9.2381723E-03 0.1749336 at 130iterations 5.1661916E-03 9.0017319E-02 at 140iterations 2.9028296E-03 6.1052322E-02 at 150iterations 1.6510113E-03 2.9350281E-02 at 160iterations 9.5997826E-04 1.7669678E-02 at 170iterations 5.7742384E-04 1.0990143E-02 at 180iterations finished qdiffx linear iterations at : 11:39:11 total time elapsed so far: 13.81000 # loops : 180 mean,max change (kT/e) : 5.7742384E-04 1.0990143E-02 energy calculations done at 13.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 11:39:11 13.954u 1.177s 0:20.60 73.3% 0+0k 0+0io 0pf+0w