Tue Oct 11 06:55:23 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 06:55:23 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2965 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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: 0.5653127 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): -18.35100 44.62300 ymin,ymax (A): 19.41100 77.06400 zmin,zma (A): -69.85400 -19.09300 x,y,z range (A): 62.97400 57.65300 50.76100 scale (grids/A): 0.5653127 object centre (A): 13.13600 48.23750 -44.47350 number of atom coordinates read : 2965 total number of charged atoms : 2819 net assigned charge : -2.554992 assigned positive charge : 433.2137 centred at (gu) : 89.62839 89.60574 89.37678 assigned negative charge : -435.7692 centred at (gu) : 89.61427 89.71157 89.34577 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6259 nv = 96 ne = 84 npr = 60879 no. pairs analyzed = 60879 no. exposed pairs = 3676 no. arc points = 26256 no. surface atoms = 1248 nbur = 1717 mkacc time = 0.1300000 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 = 1.512000 m= 276 mr = 3279 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2708 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5913249E-10 6.0099696E-11 midg,1,midg; midg,igrid,midg 1.1427198E-09 -1.5789031E-09 1,midg,midg; igrid,midg,midg -5.6522076E-10 -1.3616670E-10 gauss-seidel spectral radius is 0.9838601 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 06:55:23 rms-change max change #iterations 8.5966073E-02 13.45468 at 10iterations 6.3624405E-03 1.087925 at 20iterations 4.9386901E-04 9.1684341E-02 at 30iterations 4.9242539E-05 1.0187149E-02 at 40iterations 7.4496666E-06 1.8310547E-03 at 50iterations finished qdiffx linear iterations at : 06:55:26 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 7.4496666E-06 1.8310547E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 06:55:26 3.138u 0.141s 0:03.56 91.8% 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 Tue Oct 11 2011 at 06:55:26 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2965 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.695938 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): -18.35100 44.62300 ymin,ymax (A): 19.41100 77.06400 zmin,zma (A): -69.85400 -19.09300 x,y,z range (A): 62.97400 57.65300 50.76100 scale (grids/A): 1.695938 object centre (A): 13.13600 48.23750 -44.47350 number of atom coordinates read : 2965 total number of charged atoms : 2819 net assigned charge : -2.554992 assigned positive charge : 433.2137 centred at (gu) : 88.88461 88.81671 88.12993 assigned negative charge : -435.7692 centred at (gu) : 88.84272 89.13474 88.03696 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26256 grid for indexing accessible points = 1.400000 m= 23222 mr = 46602 m= 2868 mr = 16680 m= 83 mr = 1567 m= 0 mr = 16 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 29807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 245 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 21810 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) : 0.5653127 object centre at (A) : 13.13600 48.23750 -44.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2875800E-03 1.2672181E-02 midg,1,midg; midg,igrid,midg -3.0133454E-03 3.7282147E-03 1,midg,midg; igrid,midg,midg -8.6636674E-03 -3.2832574E-02 gauss-seidel spectral radius is 0.9983284 estimated iterations to convergence 194 setup time was (sec) 0.7900000 now iterating at: 06:55:27 rms-change max change #iterations 3.592752 155.5796 at 10iterations 1.544614 54.56110 at 20iterations 0.6670667 23.80934 at 30iterations 0.2888702 10.00084 at 40iterations 0.1248492 4.588298 at 50iterations 5.3867139E-02 1.944324 at 60iterations 2.3307104E-02 0.8054481 at 70iterations 1.0043889E-02 0.3246984 at 80iterations 4.3580243E-03 0.1517334 at 90iterations 1.8769926E-03 6.6870689E-02 at 100iterations 8.1422477E-04 2.7662277E-02 at 110iterations 3.5116790E-04 1.1793137E-02 at 120iterations finished qdiffx linear iterations at : 06:55:34 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 3.5116790E-04 1.1793137E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 06:55:35 7.449u 0.212s 0:08.16 93.7% 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 06:55:35 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2965 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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: 2.543907 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): -18.35100 44.62300 ymin,ymax (A): 19.41100 77.06400 zmin,zma (A): -69.85400 -19.09300 x,y,z range (A): 62.97400 57.65300 50.76100 scale (grids/A): 2.543907 object centre (A): 13.13600 48.23750 -44.47350 number of atom coordinates read : 2965 total number of charged atoms : 2819 net assigned charge : -2.554992 assigned positive charge : 433.2137 centred at (gu) : 88.32683 88.22483 87.19460 assigned negative charge : -435.7692 centred at (gu) : 88.26386 88.70197 87.05524 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 158752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26256 grid for indexing accessible points = 1.400000 m= 77043 mr = 113446 m= 24975 mr = 62109 m= 4787 mr = 19530 m= 411 mr = 3467 m= 14 mr = 198 m= 0 mr = 5 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 67227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 22532 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) : 1.695938 object centre at (A) : 13.13600 48.23750 -44.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5860983E-02 0.2731712 midg,1,midg; midg,igrid,midg -8.1903890E-02 7.4229538E-02 1,midg,midg; igrid,midg,midg -0.1598379 -0.4121596 gauss-seidel spectral radius is 0.9991849 estimated iterations to convergence 277 setup time was (sec) 1.520000 now iterating at: 06:55:36 rms-change max change #iterations 8.975487 262.9884 at 10iterations 5.117282 135.1946 at 20iterations 2.898221 64.93620 at 30iterations 1.637813 32.24934 at 40iterations 0.9198222 18.24822 at 50iterations 0.5176174 11.21970 at 60iterations 0.2910004 5.715714 at 70iterations 0.1630430 3.313982 at 80iterations 9.1113068E-02 1.810612 at 90iterations 5.1062308E-02 0.9710293 at 100iterations 2.8551387E-02 0.5899286 at 110iterations 1.5959863E-02 0.3362451 at 120iterations 8.9080390E-03 0.1792402 at 130iterations 4.9866918E-03 0.1007495 at 140iterations 2.7881544E-03 5.4412842E-02 at 150iterations 1.5571062E-03 3.0229568E-02 at 160iterations 8.7088958E-04 1.6349792E-02 at 170iterations 4.8722405E-04 1.1093140E-02 at 180iterations finished qdiffx linear iterations at : 06:55:46 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 4.8722405E-04 1.1093140E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 06:55:47 11.877u 0.240s 0:12.41 97.5% 0+0k 0+0io 0pf+0w