Tue Oct 11 03:26:01 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 03:26:01 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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: 0.5755768 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): -18.59100 33.71500 ymin,ymax (A): 38.65300 100.5040 zmin,zma (A): -15.90700 34.49400 x,y,z range (A): 52.30600 61.85100 50.40100 scale (grids/A): 0.5755768 object centre (A): 7.562000 69.57850 9.293499 number of atom coordinates read : 2541 total number of charged atoms : 2394 net assigned charge : 5.039021 assigned positive charge : 384.4059 centred at (gu) : 92.58940 91.32682 90.40034 assigned negative charge : -379.3676 centred at (gu) : 92.64648 91.31905 90.43142 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 50898 no. pairs analyzed = 50898 no. exposed pairs = 3264 no. arc points = 23264 no. surface atoms = 1099 nbur = 1442 mkacc time = 9.9999994E-02 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 = 1.484000 m= 222 mr = 2864 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2600000 number of dielectric boundary points 2899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2359 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3276583E-09 5.0228149E-10 midg,1,midg; midg,igrid,midg 6.1998945E-10 1.4756316E-09 1,midg,midg; igrid,midg,midg 1.0291664E-09 1.9085225E-11 gauss-seidel spectral radius is 0.9843867 estimated iterations to convergence 66 setup time was (sec) 0.4900000 now iterating at: 03:26:01 rms-change max change #iterations 9.0983003E-02 15.43982 at 10iterations 6.8465401E-03 1.086517 at 20iterations 5.2851468E-04 8.6116791E-02 at 30iterations 4.3754146E-05 7.9042912E-03 at 40iterations 5.1027200E-06 1.0032654E-03 at 50iterations finished qdiffx linear iterations at : 03:26:04 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 5.1027200E-06 1.0032654E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 03:26:05 3.252u 0.205s 0:04.17 82.7% 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 03:26:05 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.726730 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): -18.59100 33.71500 ymin,ymax (A): 38.65300 100.5040 zmin,zma (A): -15.90700 34.49400 x,y,z range (A): 52.30600 61.85100 50.40100 scale (grids/A): 1.726730 object centre (A): 7.562000 69.57850 9.293499 number of atom coordinates read : 2541 total number of charged atoms : 2394 net assigned charge : 5.039021 assigned positive charge : 384.4059 centred at (gu) : 97.76798 93.98000 91.20040 assigned negative charge : -379.3676 centred at (gu) : 97.93908 93.95709 91.29404 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60523 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 19001 mr = 40486 m= 2207 mr = 13138 m= 87 mr = 1262 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1123 time to turn everything in is 0.4300000 number of dielectric boundary points 26919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18570 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) : 0.5755768 object centre at (A) : 7.562000 69.57850 9.293499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4074355E-03 1.1286885E-02 midg,1,midg; midg,igrid,midg -1.2338930E-02 -9.4388928E-03 1,midg,midg; igrid,midg,midg 3.9563765E-04 -3.9527070E-04 gauss-seidel spectral radius is 0.9983329 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 03:26:06 rms-change max change #iterations 3.442030 146.6241 at 10iterations 1.481138 65.79891 at 20iterations 0.6403651 25.19409 at 30iterations 0.2762789 10.48450 at 40iterations 0.1192585 4.706348 at 50iterations 5.1582046E-02 1.912437 at 60iterations 2.2260582E-02 0.8500271 at 70iterations 9.6249273E-03 0.3548985 at 80iterations 4.1655311E-03 0.1544137 at 90iterations 1.7978307E-03 7.4437141E-02 at 100iterations 7.8065466E-04 3.2015920E-02 at 110iterations 3.3688921E-04 1.2827396E-02 at 120iterations finished qdiffx linear iterations at : 03:26:12 total time elapsed so far: 6.560000 # loops : 120 mean,max change (kT/e) : 3.3688921E-04 1.2827396E-02 energy calculations done at 6.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.730000 DelPhi exited at 03:26:12 6.738u 0.176s 0:07.24 95.3% 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 Tue Oct 11 2011 at 03:26:12 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 !!! WARNING: SEP 280 has a net charge of -0.4750 !!! WARNING: HIT 283 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.590096 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): -18.59100 33.71500 ymin,ymax (A): 38.65300 100.5040 zmin,zma (A): -15.90700 34.49400 x,y,z range (A): 52.30600 61.85100 50.40100 scale (grids/A): 2.590096 object centre (A): 7.562000 69.57850 9.293499 number of atom coordinates read : 2541 total number of charged atoms : 2394 net assigned charge : 5.039021 assigned positive charge : 384.4059 centred at (gu) : 101.6516 95.96990 91.80042 assigned negative charge : -379.3676 centred at (gu) : 101.9087 95.93562 91.94101 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 140369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 64998 mr = 99176 m= 19321 mr = 51299 m= 3543 mr = 14667 m= 376 mr = 2544 m= 5 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 3587 time to turn everything in is 1.080000 number of dielectric boundary points 60685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 19141 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) : 1.726730 object centre at (A) : 7.562000 69.57850 9.293499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3668542E-02 0.1979354 midg,1,midg; midg,igrid,midg -0.2042933 -0.1465244 1,midg,midg; igrid,midg,midg -2.8261580E-02 -1.0234286E-02 gauss-seidel spectral radius is 0.9991732 estimated iterations to convergence 275 setup time was (sec) 1.390000 now iterating at: 03:26:14 rms-change max change #iterations 8.617296 283.9349 at 10iterations 4.897253 121.0750 at 20iterations 2.752936 65.03290 at 30iterations 1.544813 36.94177 at 40iterations 0.8669029 20.11340 at 50iterations 0.4846815 10.75539 at 60iterations 0.2703834 6.298676 at 70iterations 0.1507213 3.173759 at 80iterations 8.4065937E-02 1.775856 at 90iterations 4.6854485E-02 1.029179 at 100iterations 2.6085893E-02 0.5809746 at 110iterations 1.4538587E-02 0.3293943 at 120iterations 8.0866786E-03 0.1707916 at 130iterations 4.4996217E-03 9.4169617E-02 at 140iterations 2.5028321E-03 5.5260658E-02 at 150iterations 1.3940835E-03 2.7702332E-02 at 160iterations 7.7705592E-04 1.6653061E-02 at 170iterations 4.3214447E-04 9.2163086E-03 at 180iterations finished qdiffx linear iterations at : 03:26:24 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 4.3214447E-04 9.2163086E-03 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 03:26:25 11.713u 0.231s 0:12.37 96.5% 0+0k 0+0io 0pf+0w