Tue Oct 11 08:21:50 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 Tue Oct 11 2011 at 08:21:50 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1176 !!! WARNING: HIT 60 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7430909 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): -6.937000 31.09100 ymin,ymax (A): 1.195000 39.63400 zmin,zma (A): -1.868000 46.04000 x,y,z range (A): 38.02800 38.43900 47.90800 scale (grids/A): 0.7430909 object centre (A): 12.07700 20.41450 22.08600 number of atom coordinates read : 1176 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 180.5651 centred at (gu) : 89.16806 89.37530 88.45027 assigned negative charge : -175.0511 centred at (gu) : 88.86467 89.34789 88.45292 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4411 nv = 96 ne = 84 npr = 23175 no. pairs analyzed = 23175 no. exposed pairs = 1491 no. arc points = 10836 no. surface atoms = 504 nbur = 672 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 2310 m= 0 mr = 52 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.2200000 number of dielectric boundary points 2322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 816 ## 61 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 4442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4200829E-07 7.9008046E-08 midg,1,midg; midg,igrid,midg 9.9966506E-08 1.0876351E-07 1,midg,midg; igrid,midg,midg -9.3370154E-08 2.3937272E-07 gauss-seidel spectral radius is 0.9904657 estimated iterations to convergence 83 setup time was (sec) 0.4100000 now iterating at: 08:21:51 rms-change max change #iterations 0.1896134 34.03532 at 10iterations 2.5649009E-02 4.364281 at 20iterations 3.4490407E-03 0.6567392 at 30iterations 4.6783630E-04 8.3808899E-02 at 40iterations 6.1822248E-05 9.2830658E-03 at 50iterations finished qdiffx linear iterations at : 08:21:53 total time elapsed so far: 2.810000 # loops : 50 mean,max change (kT/e) : 6.1822248E-05 9.2830658E-03 energy calculations done at 2.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.980000 DelPhi exited at 08:21:54 2.981u 0.166s 0:03.75 83.7% 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 Tue Oct 11 2011 at 08:21:54 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1176 !!! WARNING: HIT 60 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.229273 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): -6.937000 31.09100 ymin,ymax (A): 1.195000 39.63400 zmin,zma (A): -1.868000 46.04000 x,y,z range (A): 38.02800 38.43900 47.90800 scale (grids/A): 2.229273 object centre (A): 12.07700 20.41450 22.08600 number of atom coordinates read : 1176 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 180.5651 centred at (gu) : 87.50430 88.12603 85.35105 assigned negative charge : -175.0511 centred at (gu) : 86.59425 88.04380 85.35897 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 45893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10836 grid for indexing accessible points = 1.400000 m= 17117 mr = 30177 m= 3330 mr = 12794 m= 359 mr = 2290 m= 21 mr = 205 m= 0 mr = 13 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 0.3900000 number of dielectric boundary points 21241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8457 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) : 0.7430909 object centre at (A) : 12.07700 20.41450 22.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6544787E-02 1.2811297E-02 midg,1,midg; midg,igrid,midg 3.7319351E-02 3.5505354E-02 1,midg,midg; igrid,midg,midg -3.0662023E-02 4.0896524E-02 gauss-seidel spectral radius is 0.9988409 estimated iterations to convergence 232 setup time was (sec) 0.6500000 now iterating at: 08:21:55 rms-change max change #iterations 3.777614 214.7652 at 10iterations 1.876695 78.21030 at 20iterations 0.9294970 35.89258 at 30iterations 0.4616459 16.82617 at 40iterations 0.2291929 9.574524 at 50iterations 0.1137276 4.049828 at 60iterations 5.6253389E-02 2.077877 at 70iterations 2.7871206E-02 1.069504 at 80iterations 1.3893786E-02 0.4978142 at 90iterations 6.8663489E-03 0.2677002 at 100iterations 3.4157808E-03 0.1314192 at 110iterations 1.6855760E-03 6.1351776E-02 at 120iterations finished qdiffx linear iterations at : 08:22:01 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 1.6855760E-03 6.1351776E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 08:22:02 7.310u 0.176s 0:07.95 94.0% 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 Tue Oct 11 2011 at 08:22:02 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1176 !!! WARNING: HIT 60 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.343909 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): -6.937000 31.09100 ymin,ymax (A): 1.195000 39.63400 zmin,zma (A): -1.868000 46.04000 x,y,z range (A): 38.02800 38.43900 47.90800 scale (grids/A): 3.343909 object centre (A): 12.07700 20.41450 22.08600 number of atom coordinates read : 1176 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 180.5651 centred at (gu) : 86.25644 87.18909 83.02657 assigned negative charge : -175.0511 centred at (gu) : 84.89143 87.06572 83.03847 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 105607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10836 grid for indexing accessible points = 1.400000 m= 53106 mr = 72810 m= 21688 mr = 43547 m= 6405 mr = 17914 m= 1332 mr = 5040 m= 200 mr = 1015 m= 29 mr = 148 m= 0 mr = 26 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3344 time to turn everything in is 1.140000 number of dielectric boundary points 47867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 8488 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) : 2.229273 object centre at (A) : 12.07700 20.41450 22.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2028222 0.1333366 midg,1,midg; midg,igrid,midg 0.3309528 0.2992380 1,midg,midg; igrid,midg,midg -0.2541136 0.2790721 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 1.420000 now iterating at: 08:22:04 rms-change max change #iterations 8.168198 287.6091 at 10iterations 4.766431 151.5310 at 20iterations 2.759298 65.22263 at 30iterations 1.593233 38.89713 at 40iterations 0.9233402 20.68691 at 50iterations 0.5348837 11.14625 at 60iterations 0.3099189 6.738014 at 70iterations 0.1793816 3.990224 at 80iterations 0.1039552 2.444932 at 90iterations 6.0241394E-02 1.301891 at 100iterations 3.4946673E-02 0.7392883 at 110iterations 2.0208830E-02 0.4302444 at 120iterations 1.1727874E-02 0.2586355 at 130iterations 6.8002283E-03 0.1502781 at 140iterations 3.9383476E-03 8.3640814E-02 at 150iterations 2.2808448E-03 5.0767899E-02 at 160iterations 1.3209670E-03 2.9703140E-02 at 170iterations 7.6760811E-04 1.6433716E-02 at 180iterations finished qdiffx linear iterations at : 08:22:13 total time elapsed so far: 10.45000 # loops : 180 mean,max change (kT/e) : 7.6760811E-04 1.6433716E-02 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 08:22:13 10.616u 0.171s 0:11.19 96.3% 0+0k 0+0io 0pf+0w