Wed Feb 15 08:59:12 PST 2012 #!/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+sph_thinner.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 = amb.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 Wed Feb 15 2012 at 08:59:13 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1077 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: TPO 164 has a net charge of -1.7500 !!! WARNING: TPO 306 has a net charge of -1.7500 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: 0.5538184 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): -12.62800 51.65300 ymin,ymax (A): -54.94000 6.896000 zmin,zma (A): -22.02700 29.62000 x,y,z range (A): 64.28100 61.83600 51.64700 scale (grids/A): 0.5538184 object centre (A): 19.51250 -24.02200 3.796499 number of atom coordinates read : 3525 total number of charged atoms : 3379 net assigned charge : -2.499964 assigned positive charge : 533.3667 centred at (gu) : 89.72742 91.68616 90.00898 assigned negative charge : -535.8687 centred at (gu) : 89.68783 91.57581 89.96863 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7150 nv = 96 ne = 84 npr = 69673 no. pairs analyzed = 69673 no. exposed pairs = 4828 no. arc points = 34291 no. surface atoms = 1605 nbur = 1920 mkacc time = 0.1900000 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 = 1.540000 m= 300 mr = 3526 m= 0 mr = 11 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3577 ## 500 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9434 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6147449E-10 1.9845306E-10 midg,1,midg; midg,igrid,midg -9.4272867E-10 1.4276961E-09 1,midg,midg; igrid,midg,midg -7.0000361E-10 1.7687958E-10 gauss-seidel spectral radius is 0.9832392 estimated iterations to convergence 64 setup time was (sec) 0.6800000 now iterating at: 08:59:14 rms-change max change #iterations 8.4053226E-02 18.17024 at 10iterations 6.2732226E-03 0.9253101 at 20iterations 1.0686956E-03 0.1910095 at 30iterations 4.0206339E-04 8.1497192E-02 at 40iterations 1.6330923E-04 3.4421921E-02 at 50iterations finished qdiffx linear iterations at : 08:59:18 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 1.6330923E-04 3.4421921E-02 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 08:59:18 4.865u 0.415s 0:05.70 92.4% 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 Wed Feb 15 2012 at 08:59:18 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1077 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: TPO 164 has a net charge of -1.7500 !!! WARNING: TPO 306 has a net charge of -1.7500 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: 1.661455 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): -12.62800 51.65300 ymin,ymax (A): -54.94000 6.896000 zmin,zma (A): -22.02700 29.62000 x,y,z range (A): 64.28100 61.83600 51.64700 scale (grids/A): 1.661455 object centre (A): 19.51250 -24.02200 3.796499 number of atom coordinates read : 3525 total number of charged atoms : 3379 net assigned charge : -2.499964 assigned positive charge : 533.3667 centred at (gu) : 89.18143 95.05712 90.02581 assigned negative charge : -535.8687 centred at (gu) : 89.06282 94.72719 89.90554 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34291 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24086 mr = 52418 m= 2455 mr = 15968 m= 77 mr = 1096 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 36441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 420 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 26041 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) : 0.5538184 object centre at (A) : 19.51250 -24.02200 3.796499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0025850E-03 -4.2728232E-03 midg,1,midg; midg,igrid,midg -1.6724464E-04 1.6018867E-02 1,midg,midg; igrid,midg,midg 5.4364963E-03 1.2005480E-02 gauss-seidel spectral radius is 0.9983273 estimated iterations to convergence 194 setup time was (sec) 0.9900000 now iterating at: 08:59:20 rms-change max change #iterations 3.866130 177.1295 at 10iterations 1.665866 56.41828 at 20iterations 0.7188119 27.62918 at 30iterations 0.3109622 10.17768 at 40iterations 0.1350545 4.336863 at 50iterations 5.8385670E-02 2.000065 at 60iterations 2.5360785E-02 0.8840799 at 70iterations 1.1168064E-02 0.4024391 at 80iterations 5.0344276E-03 0.1704750 at 90iterations 2.4024334E-03 9.9525452E-02 at 100iterations 1.2767188E-03 5.4798126E-02 at 110iterations 7.8037835E-04 3.4208775E-02 at 120iterations finished qdiffx linear iterations at : 08:59:31 total time elapsed so far: 12.01000 # loops : 120 mean,max change (kT/e) : 7.8037835E-04 3.4208775E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 08:59:31 12.171u 0.452s 0:12.90 97.8% 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 Wed Feb 15 2012 at 08:59:31 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1077 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: TPO 164 has a net charge of -1.7500 !!! WARNING: TPO 306 has a net charge of -1.7500 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: 2.492183 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): -12.62800 51.65300 ymin,ymax (A): -54.94000 6.896000 zmin,zma (A): -22.02700 29.62000 x,y,z range (A): 64.28100 61.83600 51.64700 scale (grids/A): 2.492183 object centre (A): 19.51250 -24.02200 3.796499 number of atom coordinates read : 3525 total number of charged atoms : 3379 net assigned charge : -2.499964 assigned positive charge : 533.3667 centred at (gu) : 88.77188 97.58540 90.03866 assigned negative charge : -535.8687 centred at (gu) : 88.59402 97.09071 89.85830 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 184217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34291 grid for indexing accessible points = 1.400000 m= 83347 mr = 128727 m= 23374 mr = 64577 m= 3771 mr = 16921 m= 266 mr = 2286 m= 6 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 82354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 26999 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) : 1.661455 object centre at (A) : 19.51250 -24.02200 3.796499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9128422E-02 -0.1066685 midg,1,midg; midg,igrid,midg -4.6430118E-02 0.2119079 1,midg,midg; igrid,midg,midg -4.3796008E-03 0.1037273 gauss-seidel spectral radius is 0.9992117 estimated iterations to convergence 281 setup time was (sec) 1.970000 now iterating at: 08:59:34 rms-change max change #iterations 9.970826 347.5152 at 10iterations 5.785286 166.6429 at 20iterations 3.338925 76.23286 at 30iterations 1.918779 43.50385 at 40iterations 1.100158 24.50780 at 50iterations 0.6284459 13.76790 at 60iterations 0.3586447 7.975693 at 70iterations 0.2044603 4.353203 at 80iterations 0.1162094 2.420776 at 90iterations 6.6136800E-02 1.476229 at 100iterations 3.7589353E-02 0.7414560 at 110iterations 2.1277215E-02 0.4696941 at 120iterations 1.2126603E-02 0.2393112 at 130iterations 6.9133183E-03 0.1343670 at 140iterations 3.9728959E-03 8.1999779E-02 at 150iterations 2.3185776E-03 4.9777985E-02 at 160iterations 1.3877320E-03 3.5955429E-02 at 170iterations 8.7120547E-04 2.2222519E-02 at 180iterations finished qdiffx linear iterations at : 08:59:51 total time elapsed so far: 19.46000 # loops : 180 mean,max change (kT/e) : 8.7120547E-04 2.2222519E-02 energy calculations done at 19.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.61000 DelPhi exited at 08:59:52 19.618u 0.482s 0:20.45 98.2% 0+0k 0+0io 0pf+0w