Sat Oct 8 20:04:46 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 Sat Oct 8 2011 at 20:04:46 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 741 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6186570 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): -32.09500 17.56300 ymin,ymax (A): -23.61600 22.98000 zmin,zma (A): -12.45000 45.09400 x,y,z range (A): 49.65800 46.59600 57.54400 scale (grids/A): 0.6186570 object centre (A): -7.266001 -0.3179998 16.32200 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 88.72974 89.22317 89.61756 assigned negative charge : -391.9505 centred at (gu) : 88.63244 89.28287 89.50883 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6474 nv = 96 ne = 84 npr = 55095 no. pairs analyzed = 55095 no. exposed pairs = 3017 no. arc points = 21738 no. surface atoms = 1015 nbur = 1604 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3579 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.3100000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2247 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8178 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6963797E-09 8.9223811E-09 midg,1,midg; midg,igrid,midg 7.8514359E-09 -8.8483415E-10 1,midg,midg; igrid,midg,midg -4.7817146E-09 6.8017836E-09 gauss-seidel spectral radius is 0.9864661 estimated iterations to convergence 70 setup time was (sec) 0.5900000 now iterating at: 20:04:47 rms-change max change #iterations 0.1235047 20.15823 at 10iterations 1.1350830E-02 1.633895 at 20iterations 1.0239128E-03 0.1362839 at 30iterations 9.4921415E-05 1.3786316E-02 at 40iterations 8.7026729E-06 1.2588501E-03 at 50iterations finished qdiffx linear iterations at : 20:04:51 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 8.7026729E-06 1.2588501E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 20:04:51 4.471u 0.404s 0:05.13 94.9% 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 Sat Oct 8 2011 at 20:04:51 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 741 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.855971 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): -32.09500 17.56300 ymin,ymax (A): -23.61600 22.98000 zmin,zma (A): -12.45000 45.09400 x,y,z range (A): 49.65800 46.59600 57.54400 scale (grids/A): 1.855971 object centre (A): -7.266001 -0.3179998 16.32200 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 86.18871 87.66903 88.85225 assigned negative charge : -391.9505 centred at (gu) : 85.89703 87.84828 88.52643 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 23726 mr = 49616 m= 3189 mr = 17370 m= 147 mr = 1945 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 6177 time to turn everything in is 0.5700000 number of dielectric boundary points 29109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19407 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) : 0.6186570 object centre at (A) : -7.266001 -0.3179998 16.32200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1100045E-03 2.7144233E-02 midg,1,midg; midg,igrid,midg 1.3197662E-02 1.5248833E-04 1,midg,midg; igrid,midg,midg -6.0857371E-03 3.1766020E-02 gauss-seidel spectral radius is 0.9985635 estimated iterations to convergence 209 setup time was (sec) 0.8600000 now iterating at: 20:04:53 rms-change max change #iterations 4.008497 165.1042 at 10iterations 1.844704 59.59754 at 20iterations 0.8460252 30.58722 at 30iterations 0.3889080 13.06600 at 40iterations 0.1789526 5.790182 at 50iterations 8.2142964E-02 2.810368 at 60iterations 3.7819799E-02 1.168808 at 70iterations 1.7320795E-02 0.5619736 at 80iterations 7.9752225E-03 0.2660623 at 90iterations 3.6596702E-03 0.1103790 at 100iterations 1.6807463E-03 5.4708481E-02 at 110iterations 7.7426690E-04 2.6893616E-02 at 120iterations finished qdiffx linear iterations at : 20:05:02 total time elapsed so far: 10.36000 # loops : 120 mean,max change (kT/e) : 7.7426690E-04 2.6893616E-02 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.53000 DelPhi exited at 20:05:03 10.531u 0.458s 0:11.24 97.6% 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 Sat Oct 8 2011 at 20:05:03 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 741 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.783957 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): -32.09500 17.56300 ymin,ymax (A): -23.61600 22.98000 zmin,zma (A): -12.45000 45.09400 x,y,z range (A): 49.65800 46.59600 57.54400 scale (grids/A): 2.783957 object centre (A): -7.266001 -0.3179998 16.32200 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 84.28283 86.50356 88.27834 assigned negative charge : -391.9505 centred at (gu) : 83.84550 86.77230 87.78955 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 164543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 79427 mr = 120252 m= 25752 mr = 64977 m= 5528 mr = 20479 m= 703 mr = 4098 m= 43 mr = 480 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 20671 time to turn everything in is 1.440000 number of dielectric boundary points 65695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19799 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) : 1.855971 object centre at (A) : -7.266001 -0.3179998 16.32200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9212276E-02 0.3737056 midg,1,midg; midg,igrid,midg 0.1571264 1.0087858E-03 1,midg,midg; igrid,midg,midg -5.3032815E-02 0.4198070 gauss-seidel spectral radius is 0.9992324 estimated iterations to convergence 285 setup time was (sec) 1.760000 now iterating at: 20:05:05 rms-change max change #iterations 9.430803 312.7738 at 10iterations 5.399935 130.6015 at 20iterations 3.077563 66.09393 at 30iterations 1.750150 44.26917 at 40iterations 0.9970834 21.86588 at 50iterations 0.5670364 13.06409 at 60iterations 0.3225338 6.021420 at 70iterations 0.1831032 3.872002 at 80iterations 0.1043252 2.325644 at 90iterations 5.9225958E-02 1.207832 at 100iterations 3.3574667E-02 0.6257782 at 110iterations 1.9098561E-02 0.3644047 at 120iterations 1.0849444E-02 0.1975114 at 130iterations 6.1544306E-03 0.1250334 at 140iterations 3.5029140E-03 6.6974640E-02 at 150iterations 1.9898850E-03 3.6523819E-02 at 160iterations 1.1282450E-03 2.0580292E-02 at 170iterations 6.4085610E-04 1.2400627E-02 at 180iterations finished qdiffx linear iterations at : 20:05:20 total time elapsed so far: 17.31000 # loops : 180 mean,max change (kT/e) : 6.4085610E-04 1.2400627E-02 energy calculations done at 17.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.48000 DelPhi exited at 20:05:21 17.488u 0.484s 0:18.25 98.4% 0+0k 0+0io 0pf+0w