Wed Feb 15 08:55:37 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 0.6754449 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 0.6754449 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 361.6291 centred at (gu) : 90.69086 90.69264 90.26737 assigned negative charge : -359.1295 centred at (gu) : 90.88055 90.64231 90.13461 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7279 nv = 96 ne = 84 npr = 48722 no. pairs analyzed = 48722 no. exposed pairs = 2962 no. arc points = 20748 no. surface atoms = 1000 nbur = 1376 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3988 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2052 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4973346E-08 4.7639158E-08 midg,1,midg; midg,igrid,midg -3.2269345E-09 2.6845962E-08 1,midg,midg; igrid,midg,midg 5.2000999E-08 -4.8962008E-08 gauss-seidel spectral radius is 0.9886153 estimated iterations to convergence 76 setup time was (sec) 0.5900000 now iterating at: 08:55:39 rms-change max change #iterations 0.1790051 25.09067 at 10iterations 1.9840725E-02 2.777744 at 20iterations 2.3054669E-03 0.3195457 at 30iterations 3.1677869E-04 3.7649155E-02 at 40iterations 5.7838872E-05 7.7514648E-03 at 50iterations finished qdiffx linear iterations at : 08:55:42 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 5.7838872E-05 7.7514648E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 08:55:43 3.701u 0.237s 0:04.97 79.0% 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 Wed Feb 15 2012 at 08:55:43 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 = 2376 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: 2.026335 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 2.026335 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 361.6291 centred at (gu) : 92.07213 92.07725 90.80160 assigned negative charge : -359.1295 centred at (gu) : 92.64114 91.92667 90.40363 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20748 grid for indexing accessible points = 1.400000 m= 28933 mr = 53610 m= 4909 mr = 21457 m= 360 mr = 3135 m= 9 mr = 160 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 33380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17679 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) : 0.6754449 object centre at (A) : 12.97100 -5.813001 -12.62050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8400710E-03 6.7373835E-02 midg,1,midg; midg,igrid,midg 4.1915726E-02 4.9641166E-02 1,midg,midg; igrid,midg,midg 6.6848472E-03 -3.3561308E-02 gauss-seidel spectral radius is 0.9987682 estimated iterations to convergence 226 setup time was (sec) 0.9000000 now iterating at: 08:55:44 rms-change max change #iterations 4.593347 203.4818 at 10iterations 2.226913 73.55347 at 20iterations 1.088580 34.63004 at 30iterations 0.5285576 16.12272 at 40iterations 0.2568101 7.623406 at 50iterations 0.1250474 3.601577 at 60iterations 6.0955465E-02 2.015594 at 70iterations 2.9713858E-02 0.8648472 at 80iterations 1.4449562E-02 0.4561882 at 90iterations 7.0615672E-03 0.2079468 at 100iterations 3.4706153E-03 0.1121343 at 110iterations 1.7047729E-03 5.1042557E-02 at 120iterations finished qdiffx linear iterations at : 08:55:51 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 1.7047729E-03 5.1042557E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:55:51 7.612u 0.201s 0:08.44 92.5% 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 Wed Feb 15 2012 at 08:55:52 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 = 2376 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: 3.039502 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 3.039502 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 361.6291 centred at (gu) : 93.10811 93.11574 91.20229 assigned negative charge : -359.1295 centred at (gu) : 93.96168 92.89008 90.60529 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 179260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20748 grid for indexing accessible points = 1.400000 m= 92655 mr = 130016 m= 34472 mr = 75914 m= 8921 mr = 27832 m= 1621 mr = 6802 m= 152 mr = 1186 m= 8 mr = 89 m= 0 mr = 4 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 75246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 17868 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) : 2.026335 object centre at (A) : 12.97100 -5.813001 -12.62050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7186863E-02 0.8463181 midg,1,midg; midg,igrid,midg 1.186564 0.9783360 1,midg,midg; igrid,midg,midg 6.1909340E-02 -0.3759895 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.820000 now iterating at: 08:55:54 rms-change max change #iterations 10.46487 412.2474 at 10iterations 6.156915 133.0792 at 20iterations 3.622668 74.01129 at 30iterations 2.123772 39.08279 at 40iterations 1.242900 25.18182 at 50iterations 0.7274164 14.58783 at 60iterations 0.4243160 6.987003 at 70iterations 0.2477455 4.352570 at 80iterations 0.1442181 2.507843 at 90iterations 8.4129922E-02 1.445993 at 100iterations 4.8934639E-02 0.9028625 at 110iterations 2.8529391E-02 0.4822655 at 120iterations 1.6627112E-02 0.3048325 at 130iterations 9.7272545E-03 0.1766968 at 140iterations 5.7130167E-03 0.1086426 at 150iterations 3.3754881E-03 6.2026978E-02 at 160iterations 2.0151976E-03 3.6722183E-02 at 170iterations 1.2331696E-03 2.4101257E-02 at 180iterations finished qdiffx linear iterations at : 08:56:04 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 1.2331696E-03 2.4101257E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 08:56:06 12.565u 0.188s 0:14.00 91.0% 0+0k 0+0io 0pf+0w