Mon Oct 10 22:16:57 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 22:16:58 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5393449 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): 14.77200 80.77800 ymin,ymax (A): -9.947000 43.33300 zmin,zma (A): -8.021000 35.07700 x,y,z range (A): 66.00600 53.28000 43.09800 scale (grids/A): 0.5393449 object centre (A): 47.77500 16.69300 13.52800 number of atom coordinates read : 2766 total number of charged atoms : 2616 net assigned charge : 7.406028 assigned positive charge : 420.4677 centred at (gu) : 88.13313 89.72932 90.15798 assigned negative charge : -413.0622 centred at (gu) : 88.34775 89.85327 90.32454 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 5108 nv = 96 ne = 84 npr = 55714 no. pairs analyzed = 55714 no. exposed pairs = 3288 no. arc points = 23107 no. surface atoms = 1113 nbur = 1653 mkacc time = 0.1600000 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 = 1.596000 m= 194 mr = 2739 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 2548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2296 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 6690 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0712391E-09 -5.0169147E-10 midg,1,midg; midg,igrid,midg 9.8219410E-10 -2.5045821E-10 1,midg,midg; igrid,midg,midg 2.1438065E-09 -4.4653339E-10 gauss-seidel spectral radius is 0.9822593 estimated iterations to convergence 62 setup time was (sec) 0.7800000 now iterating at: 22:16:59 rms-change max change #iterations 6.9808714E-02 12.42434 at 10iterations 5.0376444E-03 0.8849297 at 20iterations 5.3510681E-04 0.1380234 at 30iterations 8.9472662E-05 2.6462555E-02 at 40iterations 1.6882845E-05 5.0582886E-03 at 50iterations finished qdiffx linear iterations at : 22:17:02 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.6882845E-05 5.0582886E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 22:17:03 4.348u 0.207s 0:05.03 90.2% 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 Mon Oct 10 2011 at 22:17:03 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 1.618035 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): 14.77200 80.77800 ymin,ymax (A): -9.947000 43.33300 zmin,zma (A): -8.021000 35.07700 x,y,z range (A): 66.00600 53.28000 43.09800 scale (grids/A): 1.618035 object centre (A): 47.77500 16.69300 13.52800 number of atom coordinates read : 2766 total number of charged atoms : 2616 net assigned charge : 7.406028 assigned positive charge : 420.4677 centred at (gu) : 84.39892 89.18753 90.47339 assigned negative charge : -413.0622 centred at (gu) : 85.04272 89.55925 90.97349 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 57983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16922 mr = 40360 m= 1539 mr = 11828 m= 36 mr = 778 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.5500000 number of dielectric boundary points 23512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19928 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) : 0.5393449 object centre at (A) : 47.77500 16.69300 13.52800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1518480E-02 2.1155251E-04 midg,1,midg; midg,igrid,midg 1.2151469E-02 -4.7795041E-03 1,midg,midg; igrid,midg,midg 5.8769039E-03 -8.3795335E-04 gauss-seidel spectral radius is 0.9981181 estimated iterations to convergence 183 setup time was (sec) 0.9100000 now iterating at: 22:17:04 rms-change max change #iterations 3.168894 170.5944 at 10iterations 1.301172 53.15634 at 20iterations 0.5313314 20.39300 at 30iterations 0.2182225 8.244577 at 40iterations 9.0300009E-02 3.586143 at 50iterations 3.7160870E-02 1.387284 at 60iterations 1.5396044E-02 0.5636678 at 70iterations 6.4196601E-03 0.2426338 at 80iterations 2.7144758E-03 0.1076317 at 90iterations 1.2040039E-03 5.2249908E-02 at 100iterations 5.6297198E-04 2.5657654E-02 at 110iterations 2.7607344E-04 1.4980316E-02 at 120iterations finished qdiffx linear iterations at : 22:17:12 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 2.7607344E-04 1.4980316E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 22:17:13 9.273u 0.223s 0:09.79 96.9% 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 Mon Oct 10 2011 at 22:17:13 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 2.427052 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): 14.77200 80.77800 ymin,ymax (A): -9.947000 43.33300 zmin,zma (A): -8.021000 35.07700 x,y,z range (A): 66.00600 53.28000 43.09800 scale (grids/A): 2.427052 object centre (A): 47.77500 16.69300 13.52800 number of atom coordinates read : 2766 total number of charged atoms : 2616 net assigned charge : 7.406028 assigned positive charge : 420.4677 centred at (gu) : 81.59838 88.78100 90.71001 assigned negative charge : -413.0622 centred at (gu) : 82.56408 89.33880 91.45995 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 134593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 60622 mr = 98069 m= 16047 mr = 48813 m= 2430 mr = 12090 m= 145 mr = 1640 m= 5 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 3030 time to turn everything in is 1.270000 number of dielectric boundary points 53180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 20895 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) : 1.618035 object centre at (A) : 47.77500 16.69300 13.52800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1599479 2.7136353E-03 midg,1,midg; midg,igrid,midg 0.1499273 -0.1208019 1,midg,midg; igrid,midg,midg -1.5781511E-02 4.2949621E-02 gauss-seidel spectral radius is 0.9991023 estimated iterations to convergence 264 setup time was (sec) 1.650000 now iterating at: 22:17:14 rms-change max change #iterations 8.011821 241.6664 at 10iterations 4.395286 108.7391 at 20iterations 2.401660 56.83799 at 30iterations 1.304308 29.81734 at 40iterations 0.7103605 15.65127 at 50iterations 0.3861146 9.019873 at 60iterations 0.2102992 4.981249 at 70iterations 0.1142377 2.528580 at 80iterations 6.1973833E-02 1.472546 at 90iterations 3.3666681E-02 0.7646294 at 100iterations 1.8327562E-02 0.4123306 at 110iterations 9.9823838E-03 0.2379456 at 120iterations 5.4619848E-03 0.1383781 at 130iterations 3.0072874E-03 6.8521500E-02 at 140iterations 1.6808243E-03 4.8732758E-02 at 150iterations 9.5879863E-04 2.6908875E-02 at 160iterations 5.6282815E-04 1.5311778E-02 at 170iterations 3.4314062E-04 1.0459900E-02 at 180iterations finished qdiffx linear iterations at : 22:17:27 total time elapsed so far: 14.45000 # loops : 180 mean,max change (kT/e) : 3.4314062E-04 1.0459900E-02 energy calculations done at 14.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.68000 DelPhi exited at 22:17:28 14.686u 0.233s 0:15.44 96.5% 0+0k 0+0io 0pf+0w