Mon Oct 10 17:13:27 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 17:13:27 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3154 !!! WARNING: HIR 148 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: 0.6108861 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): -9.297999 47.97800 ymin,ymax (A): -9.015000 43.76000 zmin,zma (A): -3.853000 54.42300 x,y,z range (A): 57.27600 52.77500 58.27600 scale (grids/A): 0.6108861 object centre (A): 19.34000 17.37250 25.28500 number of atom coordinates read : 3154 total number of charged atoms : 3012 net assigned charge : -2.985964 assigned positive charge : 478.4576 centred at (gu) : 89.67349 88.52069 89.12233 assigned negative charge : -481.4449 centred at (gu) : 89.63337 88.42447 88.99513 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 63667 no. pairs analyzed = 63667 no. exposed pairs = 4047 no. arc points = 28169 no. surface atoms = 1371 nbur = 1783 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 4223 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3600000 number of dielectric boundary points 4006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2874 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9815 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1854524E-08 5.1220321E-09 midg,1,midg; midg,igrid,midg -1.0800637E-08 3.1076424E-09 1,midg,midg; igrid,midg,midg -4.4536512E-09 8.2851848E-10 gauss-seidel spectral radius is 0.9861773 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 17:13:28 rms-change max change #iterations 0.1338569 18.19551 at 10iterations 1.1904508E-02 1.635774 at 20iterations 1.0734483E-03 0.1582298 at 30iterations 9.6523298E-05 1.4633626E-02 at 40iterations 9.7421898E-06 1.3256073E-03 at 50iterations finished qdiffx linear iterations at : 17:13:31 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 9.7421898E-06 1.3256073E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 17:13:32 3.712u 0.235s 0:04.39 89.7% 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 17:13:32 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3154 !!! WARNING: HIR 148 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: 1.832658 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): -9.297999 47.97800 ymin,ymax (A): -9.015000 43.76000 zmin,zma (A): -3.853000 54.42300 x,y,z range (A): 57.27600 52.77500 58.27600 scale (grids/A): 1.832658 object centre (A): 19.34000 17.37250 25.28500 number of atom coordinates read : 3154 total number of charged atoms : 3012 net assigned charge : -2.985964 assigned positive charge : 478.4576 centred at (gu) : 89.01975 85.56089 87.36587 assigned negative charge : -481.4449 centred at (gu) : 88.89980 85.27290 86.98524 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28169 grid for indexing accessible points = 1.400000 m= 28502 mr = 58588 m= 3769 mr = 20124 m= 180 mr = 2136 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1015 time to turn everything in is 0.6200000 number of dielectric boundary points 36978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23601 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) : 0.6108861 object centre at (A) : 19.34000 17.37250 25.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4535897E-03 1.7632797E-02 midg,1,midg; midg,igrid,midg -3.5377778E-02 4.4697095E-03 1,midg,midg; igrid,midg,midg -4.3620769E-02 2.0925125E-02 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.9100000 now iterating at: 17:13:33 rms-change max change #iterations 4.441622 167.5789 at 10iterations 2.051436 73.56158 at 20iterations 0.9426243 33.02203 at 30iterations 0.4368300 13.12169 at 40iterations 0.2002803 6.073543 at 50iterations 9.2498310E-02 2.810406 at 60iterations 4.2666994E-02 1.330844 at 70iterations 1.9649107E-02 0.6113887 at 80iterations 9.1083888E-03 0.2828827 at 90iterations 4.1879853E-03 0.1390901 at 100iterations 1.9367894E-03 5.8644772E-02 at 110iterations 8.9239905E-04 2.5182724E-02 at 120iterations finished qdiffx linear iterations at : 17:13:39 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 8.9239905E-04 2.5182724E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 17:13:40 7.656u 0.168s 0:08.33 93.7% 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 17:13:40 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3154 !!! WARNING: HIR 148 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.748987 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): -9.297999 47.97800 ymin,ymax (A): -9.015000 43.76000 zmin,zma (A): -3.853000 54.42300 x,y,z range (A): 57.27600 52.77500 58.27600 scale (grids/A): 2.748987 object centre (A): 19.34000 17.37250 25.28500 number of atom coordinates read : 3154 total number of charged atoms : 3012 net assigned charge : -2.985964 assigned positive charge : 478.4576 centred at (gu) : 88.52943 83.34119 86.04865 assigned negative charge : -481.4449 centred at (gu) : 88.34962 82.90928 85.47780 start vw surface at 0.2300000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 198155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28169 grid for indexing accessible points = 1.400000 m= 94871 mr = 142853 m= 31146 mr = 75984 m= 6343 mr = 24180 m= 734 mr = 4434 m= 31 mr = 449 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 3695 time to turn everything in is 1.620000 number of dielectric boundary points 83371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 24096 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) : 1.832658 object centre at (A) : 19.34000 17.37250 25.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2224150 6.3667834E-02 midg,1,midg; midg,igrid,midg -0.3427212 6.3074403E-02 1,midg,midg; igrid,midg,midg -0.5006006 0.3686542 gauss-seidel spectral radius is 0.9992647 estimated iterations to convergence 291 setup time was (sec) 1.950000 now iterating at: 17:13:42 rms-change max change #iterations 10.73459 292.3680 at 10iterations 6.317079 153.1774 at 20iterations 3.686782 82.88649 at 30iterations 2.143653 48.70582 at 40iterations 1.242692 24.91014 at 50iterations 0.7209439 14.63141 at 60iterations 0.4161692 8.277009 at 70iterations 0.2411549 4.602813 at 80iterations 0.1388375 2.478015 at 90iterations 8.0098525E-02 1.460722 at 100iterations 4.6212487E-02 0.8117256 at 110iterations 2.6639353E-02 0.4514256 at 120iterations 1.5348275E-02 0.2573309 at 130iterations 8.8260034E-03 0.1568489 at 140iterations 5.0807251E-03 9.0665817E-02 at 150iterations 2.9268365E-03 4.9142838E-02 at 160iterations 1.6846900E-03 2.9556274E-02 at 170iterations 9.7190210E-04 1.7375946E-02 at 180iterations finished qdiffx linear iterations at : 17:13:53 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 9.7190210E-04 1.7375946E-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 17:13:53 12.597u 0.204s 0:13.11 97.5% 0+0k 0+0io 0pf+0w