Sat Oct 8 18:13:27 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 Sat Oct 8 2011 at 18:13:27 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 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: 0.5862591 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): 8.776999 65.10000 ymin,ymax (A): -18.91600 41.80800 zmin,zma (A): 7.149000 56.40500 x,y,z range (A): 56.32300 60.72400 49.25600 scale (grids/A): 0.5862591 object centre (A): 36.93850 11.44600 31.77700 number of atom coordinates read : 3153 total number of charged atoms : 3010 net assigned charge : -0.9999948 assigned positive charge : 472.8629 centred at (gu) : 88.81231 90.64564 89.51973 assigned negative charge : -473.8641 centred at (gu) : 88.74536 90.55603 89.55915 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7301 nv = 96 ne = 84 npr = 63631 no. pairs analyzed = 63631 no. exposed pairs = 3861 no. arc points = 26401 no. surface atoms = 1295 nbur = 1858 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 = 1.456000 m= 359 mr = 4153 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3600000 number of dielectric boundary points 3491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2668 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6635622E-10 -1.2578647E-09 midg,1,midg; midg,igrid,midg -2.4695443E-09 2.6626377E-09 1,midg,midg; igrid,midg,midg -2.9252720E-09 1.2408935E-09 gauss-seidel spectral radius is 0.9849936 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 18:13:28 rms-change max change #iterations 0.1077877 15.96421 at 10iterations 8.8000838E-03 1.224215 at 20iterations 7.2347443E-04 9.5853806E-02 at 30iterations 6.6581699E-05 1.1297226E-02 at 40iterations 8.7620874E-06 1.8348694E-03 at 50iterations finished qdiffx linear iterations at : 18:13:32 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 8.7620874E-06 1.8348694E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 18:13:32 4.582u 0.378s 0:05.24 94.4% 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 18:13:32 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 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: 1.758777 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): 8.776999 65.10000 ymin,ymax (A): -18.91600 41.80800 zmin,zma (A): 7.149000 56.40500 x,y,z range (A): 56.32300 60.72400 49.25600 scale (grids/A): 1.758777 object centre (A): 36.93850 11.44600 31.77700 number of atom coordinates read : 3153 total number of charged atoms : 3010 net assigned charge : -0.9999948 assigned positive charge : 472.8629 centred at (gu) : 86.43586 91.93602 88.55810 assigned negative charge : -473.8641 centred at (gu) : 86.23593 91.66785 88.67706 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26401 grid for indexing accessible points = 1.400000 m= 29075 mr = 57013 m= 3979 mr = 21436 m= 187 mr = 2331 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23399 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) : 0.5862591 object centre at (A) : 36.93850 11.44600 31.77700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5544886E-03 -7.2209192E-03 midg,1,midg; midg,igrid,midg -3.3754803E-02 6.2376824E-03 1,midg,midg; igrid,midg,midg 3.6659064E-03 3.0141203E-02 gauss-seidel spectral radius is 0.9984577 estimated iterations to convergence 202 setup time was (sec) 0.9600000 now iterating at: 18:13:33 rms-change max change #iterations 4.059868 157.3782 at 10iterations 1.808823 62.54072 at 20iterations 0.8058865 27.77128 at 30iterations 0.3618252 11.45804 at 40iterations 0.1614471 5.533560 at 50iterations 7.2185978E-02 2.334787 at 60iterations 3.2332394E-02 0.9725170 at 70iterations 1.4470835E-02 0.4720078 at 80iterations 6.4511341E-03 0.1935849 at 90iterations 2.8970297E-03 9.8160744E-02 at 100iterations 1.2984568E-03 4.6557188E-02 at 110iterations 5.8550853E-04 1.7612934E-02 at 120iterations finished qdiffx linear iterations at : 18:13:43 total time elapsed so far: 10.42000 # loops : 120 mean,max change (kT/e) : 5.8550853E-04 1.7612934E-02 energy calculations done at 10.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.58000 DelPhi exited at 18:13:43 10.588u 0.453s 0:11.32 97.4% 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 18:13:43 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 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: 2.638166 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): 8.776999 65.10000 ymin,ymax (A): -18.91600 41.80800 zmin,zma (A): 7.149000 56.40500 x,y,z range (A): 56.32300 60.72400 49.25600 scale (grids/A): 2.638166 object centre (A): 36.93850 11.44600 31.77700 number of atom coordinates read : 3153 total number of charged atoms : 3010 net assigned charge : -0.9999948 assigned positive charge : 472.8629 centred at (gu) : 84.65369 92.90378 87.83694 assigned negative charge : -473.8641 centred at (gu) : 84.35375 92.50167 88.01550 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26401 grid for indexing accessible points = 1.400000 m= 96179 mr = 138187 m= 32282 mr = 79189 m= 6760 mr = 25631 m= 793 mr = 4926 m= 21 mr = 449 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 72991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 24069 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) : 1.758777 object centre at (A) : 36.93850 11.44600 31.77700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1488293 -8.2287431E-02 midg,1,midg; midg,igrid,midg -0.4745752 0.1430488 1,midg,midg; igrid,midg,midg -2.8927751E-02 0.3615978 gauss-seidel spectral radius is 0.9992221 estimated iterations to convergence 283 setup time was (sec) 2.020000 now iterating at: 18:13:46 rms-change max change #iterations 9.881527 290.4550 at 10iterations 5.717614 135.7998 at 20iterations 3.278276 68.52315 at 30iterations 1.873895 36.09117 at 40iterations 1.072019 20.32903 at 50iterations 0.6112641 11.06351 at 60iterations 0.3478203 6.588061 at 70iterations 0.1979303 3.645446 at 80iterations 0.1123939 2.097588 at 90iterations 6.3901328E-02 1.129874 at 100iterations 3.6264345E-02 0.6491799 at 110iterations 2.0571714E-02 0.4093232 at 120iterations 1.1690612E-02 0.2036105 at 130iterations 6.6511957E-03 0.1228714 at 140iterations 3.7851175E-03 6.8764329E-02 at 150iterations 2.1616949E-03 3.7286758E-02 at 160iterations 1.2413547E-03 2.3667932E-02 at 170iterations 7.1996503E-04 1.3496399E-02 at 180iterations finished qdiffx linear iterations at : 18:14:02 total time elapsed so far: 18.12000 # loops : 180 mean,max change (kT/e) : 7.1996503E-04 1.3496399E-02 energy calculations done at 18.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.27000 DelPhi exited at 18:14:02 18.279u 0.484s 0:19.05 98.4% 0+0k 0+0io 0pf+0w