Mon Oct 10 10:29:00 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 10:29:00 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 !!! WARNING: HIT 235 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: 0.5585365 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 0.5585365 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.01403 assigned positive charge : 415.0630 centred at (gu) : 92.16812 91.39997 86.74678 assigned negative charge : -405.0494 centred at (gu) : 92.23983 91.41670 86.53513 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5918 nv = 96 ne = 84 npr = 55230 no. pairs analyzed = 55230 no. exposed pairs = 4186 no. arc points = 30488 no. surface atoms = 1391 nbur = 1436 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 = 1.540000 m= 246 mr = 2563 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3008 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2447111E-09 1.3875388E-09 midg,1,midg; midg,igrid,midg 8.8954011E-10 1.2850236E-09 1,midg,midg; igrid,midg,midg 1.0441904E-09 6.5113759E-10 gauss-seidel spectral radius is 0.9834700 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 10:29:01 rms-change max change #iterations 7.7579126E-02 14.53734 at 10iterations 5.5363867E-03 0.8808079 at 20iterations 4.0660851E-04 6.9585800E-02 at 30iterations 3.9079408E-05 6.7324638E-03 at 40iterations 6.2223744E-06 7.7819824E-04 at 50iterations finished qdiffx linear iterations at : 10:29:04 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 6.2223744E-06 7.7819824E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 10:29:04 3.404u 0.185s 0:03.86 92.7% 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 Mon Oct 10 2011 at 10:29:04 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 !!! WARNING: HIT 235 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: 1.675610 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 1.675610 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.01403 assigned positive charge : 415.0630 centred at (gu) : 96.50381 94.19949 80.23990 assigned negative charge : -405.0494 centred at (gu) : 96.71931 94.24994 79.60516 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 19216 mr = 39001 m= 2089 mr = 12051 m= 63 mr = 890 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 33189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20586 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) : 0.5585365 object centre at (A) : 9.274999 16.02550 24.95600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9875391E-03 1.1718683E-02 midg,1,midg; midg,igrid,midg 1.5642166E-02 2.3033695E-02 1,midg,midg; igrid,midg,midg -9.7972313E-03 -1.1612895E-02 gauss-seidel spectral radius is 0.9982718 estimated iterations to convergence 191 setup time was (sec) 0.5400000 now iterating at: 10:29:05 rms-change max change #iterations 3.349289 141.6783 at 10iterations 1.417332 60.31482 at 20iterations 0.5988390 22.86490 at 30iterations 0.2547562 9.651440 at 40iterations 0.1078653 3.808999 at 50iterations 4.5676179E-02 1.743996 at 60iterations 1.9365722E-02 0.7572823 at 70iterations 8.2475282E-03 0.3136978 at 80iterations 3.5054709E-03 0.1299295 at 90iterations 1.4894152E-03 5.6905746E-02 at 100iterations 6.3181651E-04 2.2011757E-02 at 110iterations 2.7098251E-04 9.4709396E-03 at 120iterations finished qdiffx linear iterations at : 10:29:12 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.7098251E-04 9.4709396E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 10:29:12 7.764u 0.199s 0:08.31 95.6% 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 Mon Oct 10 2011 at 10:29:12 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 !!! WARNING: HIT 235 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: 2.513414 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 2.513414 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.01403 assigned positive charge : 415.0630 centred at (gu) : 99.75570 96.29914 75.35978 assigned negative charge : -405.0494 centred at (gu) : 100.0789 96.37489 74.40772 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 147543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 64652 mr = 96425 m= 19075 mr = 48071 m= 3191 mr = 13424 m= 238 mr = 1843 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 74844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21416 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) : 1.675610 object centre at (A) : 9.274999 16.02550 24.95600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7789676E-03 0.1348057 midg,1,midg; midg,igrid,midg 0.3027437 0.2828016 1,midg,midg; igrid,midg,midg -0.3321620 -0.3663641 gauss-seidel spectral radius is 0.9991674 estimated iterations to convergence 274 setup time was (sec) 1.030000 now iterating at: 10:29:14 rms-change max change #iterations 8.893368 348.9470 at 10iterations 5.171059 179.5753 at 20iterations 2.954088 86.64290 at 30iterations 1.675318 48.70776 at 40iterations 0.9460708 30.93086 at 50iterations 0.5323753 13.42944 at 60iterations 0.2985998 7.747668 at 70iterations 0.1675007 4.286293 at 80iterations 9.3443409E-02 2.234940 at 90iterations 5.2106075E-02 1.417665 at 100iterations 2.8986359E-02 0.7085838 at 110iterations 1.6178088E-02 0.3501225 at 120iterations 9.0028271E-03 0.1898212 at 130iterations 5.0094384E-03 0.1161480 at 140iterations 2.7849756E-03 6.7564011E-02 at 150iterations 1.5487703E-03 3.7234306E-02 at 160iterations 8.6004095E-04 1.9100189E-02 at 170iterations 4.7837925E-04 9.7904205E-03 at 180iterations finished qdiffx linear iterations at : 10:29:25 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 4.7837925E-04 9.7904205E-03 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 10:29:25 12.490u 0.198s 0:12.96 97.8% 0+0k 0+0io 0pf+0w