Mon Oct 10 18:28:49 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+sph.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 Mon Oct 10 2011 at 18:28:49 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN4 401 has a net charge of 1.4000 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: 0.5687628 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): 16.98300 61.97700 ymin,ymax (A): -51.19000 11.40200 zmin,zma (A): -13.55000 47.52200 x,y,z range (A): 44.99400 62.59200 61.07200 scale (grids/A): 0.5687628 object centre (A): 39.48000 -19.89400 16.98600 number of atom coordinates read : 2732 total number of charged atoms : 2583 net assigned charge : 17.10002 assigned positive charge : 408.0636 centred at (gu) : 90.24718 89.15997 88.70911 assigned negative charge : -390.9645 centred at (gu) : 90.22330 89.23980 88.78390 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5855 nv = 96 ne = 84 npr = 54598 no. pairs analyzed = 54598 no. exposed pairs = 3582 no. arc points = 25621 no. surface atoms = 1208 nbur = 1524 mkacc time = 9.0000004E-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 = 1.512000 m= 260 mr = 2950 m= 0 mr = 13 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2606 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7500 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6894697E-09 1.1127748E-09 midg,1,midg; midg,igrid,midg 4.2939807E-09 1.1735570E-09 1,midg,midg; igrid,midg,midg 2.0429072E-09 2.9580385E-09 gauss-seidel spectral radius is 0.9840344 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 18:28:49 rms-change max change #iterations 8.3361022E-02 13.78050 at 10iterations 6.3289213E-03 1.033266 at 20iterations 5.5127818E-04 8.9527130E-02 at 30iterations 7.1607967E-05 1.5629768E-02 at 40iterations 1.3531037E-05 3.1862259E-03 at 50iterations finished qdiffx linear iterations at : 18:28:52 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.3531037E-05 3.1862259E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 18:28:53 3.452u 0.181s 0:04.06 89.4% 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 Mon Oct 10 2011 at 18:28:53 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN4 401 has a net charge of 1.4000 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: 1.706288 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): 16.98300 61.97700 ymin,ymax (A): -51.19000 11.40200 zmin,zma (A): -13.55000 47.52200 x,y,z range (A): 44.99400 62.59200 61.07200 scale (grids/A): 1.706288 object centre (A): 39.48000 -19.89400 16.98600 number of atom coordinates read : 2732 total number of charged atoms : 2583 net assigned charge : 17.10002 assigned positive charge : 408.0636 centred at (gu) : 90.74066 87.47890 86.12657 assigned negative charge : -390.9645 centred at (gu) : 90.66969 87.71928 86.35142 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25621 grid for indexing accessible points = 1.400000 m= 20453 mr = 42486 m= 2330 mr = 14027 m= 77 mr = 1159 m= 0 mr = 10 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1417 time to turn everything in is 0.3300000 number of dielectric boundary points 29233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20009 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) : 0.5687628 object centre at (A) : 39.48000 -19.89400 16.98600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9533736E-02 1.4987697E-02 midg,1,midg; midg,igrid,midg 4.8182616E-03 1.7145555E-02 1,midg,midg; igrid,midg,midg 1.2792676E-02 1.8828778E-02 gauss-seidel spectral radius is 0.9983189 estimated iterations to convergence 194 setup time was (sec) 0.5500000 now iterating at: 18:28:53 rms-change max change #iterations 3.405475 175.1321 at 10iterations 1.458811 54.63853 at 20iterations 0.6282958 22.42243 at 30iterations 0.2690412 9.958513 at 40iterations 0.1156625 4.114175 at 50iterations 4.9864173E-02 1.838253 at 60iterations 2.1447806E-02 0.7490968 at 70iterations 9.2223743E-03 0.3107262 at 80iterations 3.9911205E-03 0.1365871 at 90iterations 1.7345063E-03 6.6566467E-02 at 100iterations 7.5361063E-04 2.7168274E-02 at 110iterations 3.2881755E-04 1.1668980E-02 at 120iterations finished qdiffx linear iterations at : 18:29:01 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.2881755E-04 1.1668980E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 18:29:01 7.878u 0.203s 0:08.39 96.1% 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 Mon Oct 10 2011 at 18:29:01 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN4 401 has a net charge of 1.4000 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: 2.559433 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): 16.98300 61.97700 ymin,ymax (A): -51.19000 11.40200 zmin,zma (A): -13.55000 47.52200 x,y,z range (A): 44.99400 62.59200 61.07200 scale (grids/A): 2.559433 object centre (A): 39.48000 -19.89400 16.98600 number of atom coordinates read : 2732 total number of charged atoms : 2583 net assigned charge : 17.10002 assigned positive charge : 408.0636 centred at (gu) : 91.11083 86.21825 84.18966 assigned negative charge : -390.9645 centred at (gu) : 91.00436 86.57899 84.52711 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25621 grid for indexing accessible points = 1.400000 m= 69622 mr = 104341 m= 20760 mr = 54877 m= 3747 mr = 15381 m= 312 mr = 2450 m= 12 mr = 143 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4970 time to turn everything in is 0.8200000 number of dielectric boundary points 65839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20650 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) : 1.706288 object centre at (A) : 39.48000 -19.89400 16.98600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8178670 0.2562065 midg,1,midg; midg,igrid,midg 2.0563480E-02 0.3783892 1,midg,midg; igrid,midg,midg 0.1666145 0.2291075 gauss-seidel spectral radius is 0.9991733 estimated iterations to convergence 275 setup time was (sec) 1.050000 now iterating at: 18:29:02 rms-change max change #iterations 8.730450 293.4854 at 10iterations 5.020165 136.0821 at 20iterations 2.852701 76.79905 at 30iterations 1.613278 35.24024 at 40iterations 0.9071051 20.00473 at 50iterations 0.5094827 11.21611 at 60iterations 0.2850066 6.263333 at 70iterations 0.1591741 3.571503 at 80iterations 8.8875689E-02 2.109226 at 90iterations 4.9580093E-02 1.102776 at 100iterations 2.7648553E-02 0.5792770 at 110iterations 1.5371919E-02 0.3002243 at 120iterations 8.5824570E-03 0.1826439 at 130iterations 4.7732005E-03 0.1015396 at 140iterations 2.6636454E-03 6.2927246E-02 at 150iterations 1.4829811E-03 3.0937195E-02 at 160iterations 8.2569139E-04 1.6124725E-02 at 170iterations 4.6064868E-04 9.7818375E-03 at 180iterations finished qdiffx linear iterations at : 18:29:14 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 4.6064868E-04 9.7818375E-03 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 18:29:14 12.636u 0.194s 0:13.14 97.5% 0+0k 0+0io 0pf+0w