Tue Oct 11 08:37:34 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 08:37:34 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 43 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6489009 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): -11.03600 37.32300 ymin,ymax (A): -25.87800 22.28700 zmin,zma (A): -8.748000 46.11400 x,y,z range (A): 48.35900 48.16500 54.86200 scale (grids/A): 0.6489009 object centre (A): 13.14350 -1.795501 18.68300 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.514024 assigned positive charge : 418.7406 centred at (gu) : 89.99557 90.37158 91.20669 assigned negative charge : -415.2273 centred at (gu) : 89.75710 90.22301 91.25607 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7761 nv = 96 ne = 84 npr = 56670 no. pairs analyzed = 56670 no. exposed pairs = 3388 no. arc points = 23606 no. surface atoms = 1140 nbur = 1862 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4333 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1218556E-08 -1.6880516E-09 midg,1,midg; midg,igrid,midg -1.5893653E-08 3.2263578E-08 1,midg,midg; igrid,midg,midg -3.2116510E-08 4.3413170E-08 gauss-seidel spectral radius is 0.9877056 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 08:37:35 rms-change max change #iterations 0.1601320 24.57737 at 10iterations 1.6966300E-02 2.882161 at 20iterations 1.8434571E-03 0.2544365 at 30iterations 2.4139915E-04 3.8169861E-02 at 40iterations 4.8415037E-05 8.0871582E-03 at 50iterations finished qdiffx linear iterations at : 08:37:37 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.8415037E-05 8.0871582E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:37:38 3.428u 0.139s 0:04.07 87.2% 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 08:37:38 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 43 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.946703 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): -11.03600 37.32300 ymin,ymax (A): -25.87800 22.28700 zmin,zma (A): -8.748000 46.11400 x,y,z range (A): 48.35900 48.16500 54.86200 scale (grids/A): 1.946703 object centre (A): 13.14350 -1.795501 18.68300 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.514024 assigned positive charge : 418.7406 centred at (gu) : 89.98605 91.11409 93.61951 assigned negative charge : -415.2273 centred at (gu) : 89.27085 90.66898 93.76791 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 83877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23606 grid for indexing accessible points = 1.400000 m= 30464 mr = 58999 m= 4660 mr = 22589 m= 299 mr = 2942 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 293 time to turn everything in is 0.6300000 number of dielectric boundary points 34665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20443 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) : 0.6489009 object centre at (A) : 13.14350 -1.795501 18.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0892450E-03 -1.4560672E-02 midg,1,midg; midg,igrid,midg -1.0685956E-02 2.6520131E-02 1,midg,midg; igrid,midg,midg -1.2867480E-02 6.0220554E-02 gauss-seidel spectral radius is 0.9987095 estimated iterations to convergence 221 setup time was (sec) 0.9200000 now iterating at: 08:37:39 rms-change max change #iterations 4.627779 195.0315 at 10iterations 2.223030 68.29131 at 20iterations 1.063493 32.12069 at 30iterations 0.5095669 14.79151 at 40iterations 0.2443256 7.827082 at 50iterations 0.1171234 3.339325 at 60iterations 5.6277018E-02 1.611496 at 70iterations 2.6910663E-02 0.8319159 at 80iterations 1.2877886E-02 0.3892250 at 90iterations 6.2043802E-03 0.1903811 at 100iterations 2.9853340E-03 9.9357605E-02 at 110iterations 1.4500691E-03 4.5776367E-02 at 120iterations finished qdiffx linear iterations at : 08:37:46 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.4500691E-03 4.5776367E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 08:37:46 7.537u 0.167s 0:08.24 93.3% 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 08:37:46 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 43 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.920054 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): -11.03600 37.32300 ymin,ymax (A): -25.87800 22.28700 zmin,zma (A): -8.748000 46.11400 x,y,z range (A): 48.35900 48.16500 54.86200 scale (grids/A): 2.920054 object centre (A): 13.14350 -1.795501 18.68300 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.514024 assigned positive charge : 418.7406 centred at (gu) : 89.97887 91.67088 95.42918 assigned negative charge : -415.2273 centred at (gu) : 88.90626 91.00333 95.65170 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 193933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23606 grid for indexing accessible points = 1.400000 m= 99450 mr = 142709 m= 35621 mr = 81807 m= 8532 mr = 28765 m= 1248 mr = 6374 m= 87 mr = 844 m= 0 mr = 39 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 1071 time to turn everything in is 1.580000 number of dielectric boundary points 78333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 20880 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) : 1.946703 object centre at (A) : 13.14350 -1.795501 18.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1761185 3.6760341E-02 midg,1,midg; midg,igrid,midg -0.1347750 0.3254967 1,midg,midg; igrid,midg,midg -8.5585870E-02 0.5410664 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 1.880000 now iterating at: 08:37:48 rms-change max change #iterations 10.58631 373.8748 at 10iterations 6.212087 133.5578 at 20iterations 3.627231 79.88638 at 30iterations 2.114621 43.16989 at 40iterations 1.231646 23.96580 at 50iterations 0.7172371 12.65104 at 60iterations 0.4164199 7.299150 at 70iterations 0.2417031 4.432000 at 80iterations 0.1405584 2.451395 at 90iterations 8.1354633E-02 1.396597 at 100iterations 4.7248095E-02 0.8286743 at 110iterations 2.7408468E-02 0.4822640 at 120iterations 1.5958551E-02 0.3032990 at 130iterations 9.2604998E-03 0.1528130 at 140iterations 5.4200990E-03 9.3524933E-02 at 150iterations 3.1829567E-03 5.5401325E-02 at 160iterations 1.8967310E-03 3.4372330E-02 at 170iterations 1.1464689E-03 2.1163940E-02 at 180iterations finished qdiffx linear iterations at : 08:37:59 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 1.1464689E-03 2.1163940E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 08:38:00 12.380u 0.171s 0:13.05 96.1% 0+0k 0+0io 0pf+0w