Tue Oct 11 00:32:46 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 00:32:46 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 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: 0.5843346 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): 20.00700 80.93100 ymin,ymax (A): -0.8860000 39.73700 zmin,zma (A): -6.972000 41.85500 x,y,z range (A): 60.92400 40.62300 48.82700 scale (grids/A): 0.5843346 object centre (A): 50.46900 19.42550 17.44150 number of atom coordinates read : 2048 total number of charged atoms : 1908 net assigned charge : 2.000002 assigned positive charge : 300.0928 centred at (gu) : 88.92229 89.98888 89.63917 assigned negative charge : -298.0930 centred at (gu) : 88.97429 90.15163 89.67850 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4634 nv = 96 ne = 84 npr = 41286 no. pairs analyzed = 41286 no. exposed pairs = 2629 no. arc points = 19003 no. surface atoms = 885 nbur = 1163 mkacc time = 0.1400000 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= 201 mr = 2392 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3100000 number of dielectric boundary points 2437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 5784 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2640374E-09 -1.5972111E-10 midg,1,midg; midg,igrid,midg 3.2214256E-09 -2.3211293E-09 1,midg,midg; igrid,midg,midg 1.7704251E-09 -3.0079786E-10 gauss-seidel spectral radius is 0.9848071 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 00:32:47 rms-change max change #iterations 8.4496155E-02 16.31713 at 10iterations 6.5532490E-03 1.257503 at 20iterations 5.0906726E-04 8.5939348E-02 at 30iterations 4.0849143E-05 9.0847015E-03 at 40iterations 3.2327271E-06 5.6648254E-04 at 50iterations finished qdiffx linear iterations at : 00:32:50 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 3.2327271E-06 5.6648254E-04 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 00:32:51 4.380u 0.429s 0:05.18 92.6% 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 00:32:51 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 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: 1.753004 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): 20.00700 80.93100 ymin,ymax (A): -0.8860000 39.73700 zmin,zma (A): -6.972000 41.85500 x,y,z range (A): 60.92400 40.62300 48.82700 scale (grids/A): 1.753004 object centre (A): 50.46900 19.42550 17.44150 number of atom coordinates read : 2048 total number of charged atoms : 1908 net assigned charge : 2.000002 assigned positive charge : 300.0928 centred at (gu) : 86.76651 89.96674 88.91738 assigned negative charge : -298.0930 centred at (gu) : 86.92280 90.45476 89.03548 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 50907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19003 grid for indexing accessible points = 1.400000 m= 16410 mr = 33942 m= 2029 mr = 11622 m= 73 mr = 1133 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2696 time to turn everything in is 0.5200000 number of dielectric boundary points 22722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14887 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) : 0.5843346 object centre at (A) : 50.46900 19.42550 17.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0558971E-02 1.6231835E-03 midg,1,midg; midg,igrid,midg 6.3604959E-03 1.6373392E-03 1,midg,midg; igrid,midg,midg -6.8321652E-03 2.8035932E-03 gauss-seidel spectral radius is 0.9983343 estimated iterations to convergence 194 setup time was (sec) 0.8300000 now iterating at: 00:32:52 rms-change max change #iterations 3.107793 152.8195 at 10iterations 1.339159 57.33228 at 20iterations 0.5767545 25.91093 at 30iterations 0.2487789 10.22995 at 40iterations 0.1074582 4.353280 at 50iterations 4.6409409E-02 1.723705 at 60iterations 2.0109123E-02 0.9128151 at 70iterations 8.6787827E-03 0.3293200 at 80iterations 3.7477154E-03 0.1567745 at 90iterations 1.6235983E-03 6.3342094E-02 at 100iterations 6.9970102E-04 2.9579163E-02 at 110iterations 3.0228827E-04 1.3036728E-02 at 120iterations finished qdiffx linear iterations at : 00:33:01 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 3.0228827E-04 1.3036728E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 00:33:02 9.762u 0.464s 0:10.81 94.5% 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 Tue Oct 11 2011 at 00:33:02 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 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: 2.629506 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): 20.00700 80.93100 ymin,ymax (A): -0.8860000 39.73700 zmin,zma (A): -6.972000 41.85500 x,y,z range (A): 60.92400 40.62300 48.82700 scale (grids/A): 2.629506 object centre (A): 50.46900 19.42550 17.44150 number of atom coordinates read : 2048 total number of charged atoms : 1908 net assigned charge : 2.000002 assigned positive charge : 300.0928 centred at (gu) : 85.14980 89.94971 88.37605 assigned negative charge : -298.0930 centred at (gu) : 85.38416 90.68221 88.55322 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 117845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19003 grid for indexing accessible points = 1.400000 m= 54923 mr = 82654 m= 17664 mr = 43762 m= 3429 mr = 13806 m= 296 mr = 2422 m= 4 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 8959 time to turn everything in is 1.350000 number of dielectric boundary points 51378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 15260 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) : 1.753004 object centre at (A) : 50.46900 19.42550 17.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1705841 4.9088681E-03 midg,1,midg; midg,igrid,midg 7.3212273E-02 6.4958341E-02 1,midg,midg; igrid,midg,midg -8.9902215E-02 9.3831532E-02 gauss-seidel spectral radius is 0.9991608 estimated iterations to convergence 273 setup time was (sec) 1.690000 now iterating at: 00:33:04 rms-change max change #iterations 7.590285 298.2648 at 10iterations 4.227155 126.7166 at 20iterations 2.342485 79.20483 at 30iterations 1.298239 31.81404 at 40iterations 0.7173232 17.55307 at 50iterations 0.3984174 9.228157 at 60iterations 0.2198580 4.643489 at 70iterations 0.1216516 2.691280 at 80iterations 6.7279488E-02 1.545732 at 90iterations 3.7227213E-02 0.8110371 at 100iterations 2.0485269E-02 0.4483843 at 110iterations 1.1356723E-02 0.2949219 at 120iterations 6.2684589E-03 0.1415024 at 130iterations 3.4586017E-03 7.7529907E-02 at 140iterations 1.9178493E-03 4.6696231E-02 at 150iterations 1.0590428E-03 2.2058129E-02 at 160iterations 5.8635126E-04 1.2893677E-02 at 170iterations 3.2307746E-04 7.1105957E-03 at 180iterations finished qdiffx linear iterations at : 00:33:18 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 3.2307746E-04 7.1105957E-03 energy calculations done at 15.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.09000 DelPhi exited at 00:33:19 16.091u 0.492s 0:16.87 98.2% 0+0k 0+0io 0pf+0w