Tue Oct 11 03:25:45 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 Tue Oct 11 2011 at 03:25:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6075500 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): -19.56500 26.44200 ymin,ymax (A): -16.90900 41.68700 zmin,zma (A): -24.75500 25.16500 x,y,z range (A): 46.00700 58.59600 49.92000 scale (grids/A): 0.6075500 object centre (A): 3.438499 12.38900 0.2050009 number of atom coordinates read : 2473 total number of charged atoms : 2324 net assigned charge : 5.9306622E-06 assigned positive charge : 360.0560 centred at (gu) : 90.83217 90.50213 88.89732 assigned negative charge : -360.0567 centred at (gu) : 90.85733 90.66996 89.08943 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6307 nv = 96 ne = 84 npr = 48205 no. pairs analyzed = 48205 no. exposed pairs = 3554 no. arc points = 25759 no. surface atoms = 1172 nbur = 1301 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3007 m= 0 mr = 16 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2800000 number of dielectric boundary points 3585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2519 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0267717E-08 -6.5352546E-09 midg,1,midg; midg,igrid,midg 6.2211982E-09 -8.2155012E-09 1,midg,midg; igrid,midg,midg 8.5454349E-10 -1.3441700E-09 gauss-seidel spectral radius is 0.9859812 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 03:25:45 rms-change max change #iterations 0.1129283 18.70930 at 10iterations 9.4610574E-03 1.474792 at 20iterations 8.2559336E-04 0.1268951 at 30iterations 7.3688236E-05 1.3870239E-02 at 40iterations 6.3931238E-06 1.1857748E-03 at 50iterations finished qdiffx linear iterations at : 03:25:48 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 6.3931238E-06 1.1857748E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 03:25:49 3.274u 0.191s 0:03.83 90.3% 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 03:25:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.822650 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): -19.56500 26.44200 ymin,ymax (A): -16.90900 41.68700 zmin,zma (A): -24.75500 25.16500 x,y,z range (A): 46.00700 58.59600 49.92000 scale (grids/A): 1.822650 object centre (A): 3.438499 12.38900 0.2050009 number of atom coordinates read : 2473 total number of charged atoms : 2324 net assigned charge : 5.9306622E-06 assigned positive charge : 360.0560 centred at (gu) : 92.49575 91.50571 86.69160 assigned negative charge : -360.0567 centred at (gu) : 92.57198 92.00958 87.26802 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 67956 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 21366 mr = 43371 m= 2605 mr = 14130 m= 90 mr = 1174 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 699 time to turn everything in is 0.4700000 number of dielectric boundary points 33327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 18216 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) : 0.6075500 object centre at (A) : 3.438499 12.38900 0.2050009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8484220E-02 -1.7346038E-02 midg,1,midg; midg,igrid,midg 7.3033292E-03 -1.6897207E-02 1,midg,midg; igrid,midg,midg 4.6683429E-03 3.1829872E-03 gauss-seidel spectral radius is 0.9985209 estimated iterations to convergence 206 setup time was (sec) 0.7600000 now iterating at: 03:25:50 rms-change max change #iterations 3.725974 184.9066 at 10iterations 1.681226 60.68735 at 20iterations 0.7590668 26.63629 at 30iterations 0.3441209 14.90789 at 40iterations 0.1556015 4.867634 at 50iterations 7.0501901E-02 2.372613 at 60iterations 3.2089025E-02 1.071257 at 70iterations 1.4521582E-02 0.4908675 at 80iterations 6.5950095E-03 0.2309971 at 90iterations 2.9865380E-03 0.1106706 at 100iterations 1.3545320E-03 4.9056530E-02 at 110iterations 6.1491539E-04 2.3506165E-02 at 120iterations finished qdiffx linear iterations at : 03:25:56 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 6.1491539E-04 2.3506165E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 03:25:57 7.440u 0.263s 0:08.18 94.1% 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 Tue Oct 11 2011 at 03:25:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.733975 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): -19.56500 26.44200 ymin,ymax (A): -16.90900 41.68700 zmin,zma (A): -24.75500 25.16500 x,y,z range (A): 46.00700 58.59600 49.92000 scale (grids/A): 2.733975 object centre (A): 3.438499 12.38900 0.2050009 number of atom coordinates read : 2473 total number of charged atoms : 2324 net assigned charge : 5.9306622E-06 assigned positive charge : 360.0560 centred at (gu) : 93.74352 92.25837 85.03732 assigned negative charge : -360.0567 centred at (gu) : 93.85777 93.01436 85.90201 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 157273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 71665 mr = 106612 m= 22258 mr = 55215 m= 4138 mr = 16073 m= 398 mr = 2546 m= 14 mr = 167 m= 0 mr = 5 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2408 time to turn everything in is 1.180000 number of dielectric boundary points 75128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 18581 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) : 1.822650 object centre at (A) : 3.438499 12.38900 0.2050009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1925396 -0.1675769 midg,1,midg; midg,igrid,midg 2.7684320E-02 0.1855327 1,midg,midg; igrid,midg,midg 4.4535790E-02 1.7921530E-02 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 1.490000 now iterating at: 03:25:59 rms-change max change #iterations 9.044360 271.3552 at 10iterations 5.293180 130.9169 at 20iterations 3.064327 68.86891 at 30iterations 1.769101 39.03610 at 40iterations 1.015840 23.40808 at 50iterations 0.5823054 12.81142 at 60iterations 0.3339996 6.897418 at 70iterations 0.1912446 3.969917 at 80iterations 0.1093244 2.380799 at 90iterations 6.2337074E-02 1.195629 at 100iterations 3.5539251E-02 0.6896391 at 110iterations 2.0222941E-02 0.4073083 at 120iterations 1.1560149E-02 0.2293930 at 130iterations 6.6010426E-03 0.1271667 at 140iterations 3.7517359E-03 7.4172974E-02 at 150iterations 2.1361795E-03 4.4273376E-02 at 160iterations 1.2149130E-03 2.2941589E-02 at 170iterations 6.9274497E-04 1.3902783E-02 at 180iterations finished qdiffx linear iterations at : 03:26:10 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 6.9274497E-04 1.3902783E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 03:26:10 12.591u 0.211s 0:13.08 97.8% 0+0k 0+0io 0pf+0w