Mon Oct 10 20:16:18 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 Mon Oct 10 2011 at 20:16:18 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 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 !!! WARNING: HIR 102 has a net charge of 0.5140 !!! WARNING: HIR 228 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6187968 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): -10.48000 45.43200 ymin,ymax (A): -16.93200 36.23800 zmin,zma (A): -12.05000 45.48100 x,y,z range (A): 55.91200 53.17000 57.53100 scale (grids/A): 0.6187968 object centre (A): 17.47600 9.653000 16.71550 number of atom coordinates read : 2532 total number of charged atoms : 2395 net assigned charge : -3.971988 assigned positive charge : 376.5489 centred at (gu) : 89.21744 90.55746 90.39584 assigned negative charge : -380.5219 centred at (gu) : 89.14114 90.66488 90.29527 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6662 nv = 96 ne = 84 npr = 49958 no. pairs analyzed = 49958 no. exposed pairs = 3585 no. arc points = 25552 no. surface atoms = 1186 nbur = 1346 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3274 m= 6 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2497 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8020 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6241299E-09 3.5571341E-09 midg,1,midg; midg,igrid,midg 3.2123595E-09 -1.1151067E-08 1,midg,midg; igrid,midg,midg -9.3401678E-09 1.4387488E-09 gauss-seidel spectral radius is 0.9864861 estimated iterations to convergence 70 setup time was (sec) 0.3800000 now iterating at: 20:16:18 rms-change max change #iterations 0.1220583 19.68311 at 10iterations 1.1271464E-02 1.687782 at 20iterations 1.0197067E-03 0.1654816 at 30iterations 9.2282025E-05 1.4650345E-02 at 40iterations 8.7038115E-06 1.4429092E-03 at 50iterations finished qdiffx linear iterations at : 20:16:21 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 8.7038115E-06 1.4429092E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 20:16:22 3.392u 0.177s 0:04.05 87.9% 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 20:16:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 !!! WARNING: HIR 102 has a net charge of 0.5140 !!! WARNING: HIR 228 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.856390 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): -10.48000 45.43200 ymin,ymax (A): -16.93200 36.23800 zmin,zma (A): -12.05000 45.48100 x,y,z range (A): 55.91200 53.17000 57.53100 scale (grids/A): 1.856390 object centre (A): 17.47600 9.653000 16.71550 number of atom coordinates read : 2532 total number of charged atoms : 2395 net assigned charge : -3.971988 assigned positive charge : 376.5489 centred at (gu) : 87.65186 91.67188 91.18703 assigned negative charge : -380.5219 centred at (gu) : 87.42336 91.99471 90.88555 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25552 grid for indexing accessible points = 1.400000 m= 24841 mr = 46522 m= 3780 mr = 17164 m= 216 mr = 2055 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 34622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18776 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) : 0.6187968 object centre at (A) : 17.47600 9.653000 16.71550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1775171E-02 -1.7751148E-02 midg,1,midg; midg,igrid,midg 1.4499458E-02 -2.8615227E-02 1,midg,midg; igrid,midg,midg -5.9866053E-03 9.9768362E-04 gauss-seidel spectral radius is 0.9985836 estimated iterations to convergence 211 setup time was (sec) 0.5800000 now iterating at: 20:16:23 rms-change max change #iterations 4.039256 191.3278 at 10iterations 1.848131 74.32446 at 20iterations 0.8504214 29.10789 at 30iterations 0.3927963 13.18994 at 40iterations 0.1808226 6.217276 at 50iterations 8.3078131E-02 3.089468 at 60iterations 3.8255312E-02 1.429822 at 70iterations 1.7675394E-02 0.5847287 at 80iterations 8.1712818E-03 0.2882939 at 90iterations 3.7606340E-03 0.1172192 at 100iterations 1.7365344E-03 6.0543060E-02 at 110iterations 8.0078444E-04 3.0282974E-02 at 120iterations finished qdiffx linear iterations at : 20:16:30 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 8.0078444E-04 3.0282974E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 20:16:30 7.850u 0.189s 0:08.50 94.4% 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 20:16:31 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 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 !!! WARNING: HIR 102 has a net charge of 0.5140 !!! WARNING: HIR 228 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.784586 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): -10.48000 45.43200 ymin,ymax (A): -16.93200 36.23800 zmin,zma (A): -12.05000 45.48100 x,y,z range (A): 55.91200 53.17000 57.53100 scale (grids/A): 2.784586 object centre (A): 17.47600 9.653000 16.71550 number of atom coordinates read : 2532 total number of charged atoms : 2395 net assigned charge : -3.971988 assigned positive charge : 376.5489 centred at (gu) : 86.47775 92.50772 91.78040 assigned negative charge : -380.5219 centred at (gu) : 86.13506 92.99213 91.32842 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25552 grid for indexing accessible points = 1.400000 m= 79072 mr = 113863 m= 28659 mr = 61961 m= 6620 mr = 21833 m= 788 mr = 4429 m= 31 mr = 474 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 78192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19160 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) : 1.856390 object centre at (A) : 17.47600 9.653000 16.71550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1503723 -0.1602496 midg,1,midg; midg,igrid,midg 0.1955965 -0.2260914 1,midg,midg; igrid,midg,midg 0.1162542 -9.3905628E-04 gauss-seidel spectral radius is 0.9992574 estimated iterations to convergence 290 setup time was (sec) 1.160000 now iterating at: 20:16:32 rms-change max change #iterations 9.795080 302.2377 at 10iterations 5.813420 176.6241 at 20iterations 3.410208 81.89017 at 30iterations 1.998766 46.39422 at 40iterations 1.159991 28.71438 at 50iterations 0.6720092 15.87817 at 60iterations 0.3884769 7.801352 at 70iterations 0.2240103 4.986091 at 80iterations 0.1286894 2.570477 at 90iterations 7.4144118E-02 1.396890 at 100iterations 4.2644747E-02 0.8368683 at 110iterations 2.4485104E-02 0.5305764 at 120iterations 1.4036338E-02 0.2653389 at 130iterations 8.0852760E-03 0.1637840 at 140iterations 4.6489490E-03 9.0263367E-02 at 150iterations 2.6657295E-03 5.7636380E-02 at 160iterations 1.5299452E-03 2.8953552E-02 at 170iterations 8.8070217E-04 1.8024445E-02 at 180iterations finished qdiffx linear iterations at : 20:16:43 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 8.8070217E-04 1.8024445E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 20:16:44 12.728u 0.194s 0:13.23 97.5% 0+0k 0+0io 0pf+0w