Mon Oct 10 10:24:57 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 10:24:57 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2626 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: 0.5879341 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): -17.80700 31.80100 ymin,ymax (A): -60.05300 -2.845000 zmin,zma (A): -0.4200000 60.13100 x,y,z range (A): 49.60800 57.20800 60.55100 scale (grids/A): 0.5879341 object centre (A): 6.997000 -31.44900 29.85550 number of atom coordinates read : 2626 total number of charged atoms : 2481 net assigned charge : 9.000021 assigned positive charge : 385.2632 centred at (gu) : 88.56964 88.50050 87.70840 assigned negative charge : -376.2636 centred at (gu) : 88.61519 88.33170 87.67667 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6274 nv = 96 ne = 84 npr = 50184 no. pairs analyzed = 50184 no. exposed pairs = 4076 no. arc points = 29664 no. surface atoms = 1341 nbur = 1285 mkacc time = 0.1300000 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 = 1.484000 m= 326 mr = 2695 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2886 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1079388E-09 2.0262203E-09 midg,1,midg; midg,igrid,midg -2.1821314E-09 4.6672146E-09 1,midg,midg; igrid,midg,midg 5.1478559E-09 1.1299220E-09 gauss-seidel spectral radius is 0.9850573 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 10:24:58 rms-change max change #iterations 9.5548138E-02 16.19894 at 10iterations 7.5473948E-03 1.401840 at 20iterations 6.2662980E-04 0.1263046 at 30iterations 5.7121924E-05 1.0926247E-02 at 40iterations 8.2654306E-06 1.2741089E-03 at 50iterations finished qdiffx linear iterations at : 10:25:02 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 8.2654306E-06 1.2741089E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 10:25:02 4.514u 0.369s 0:05.27 92.4% 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 Mon Oct 10 2011 at 10:25:02 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2626 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: 1.763802 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): -17.80700 31.80100 ymin,ymax (A): -60.05300 -2.845000 zmin,zma (A): -0.4200000 60.13100 x,y,z range (A): 49.60800 57.20800 60.55100 scale (grids/A): 1.763802 object centre (A): 6.997000 -31.44900 29.85550 number of atom coordinates read : 2626 total number of charged atoms : 2481 net assigned charge : 9.000021 assigned positive charge : 385.2632 centred at (gu) : 85.70844 85.50097 83.12507 assigned negative charge : -376.2636 centred at (gu) : 85.84537 84.99490 83.02982 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29664 grid for indexing accessible points = 1.400000 m= 21530 mr = 40284 m= 2889 mr = 13596 m= 127 mr = 1198 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 36065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 243 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19305 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) : 0.5879341 object centre at (A) : 6.997000 -31.44900 29.85550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8402580E-02 6.4668036E-03 midg,1,midg; midg,igrid,midg 1.5047045E-02 3.2391731E-02 1,midg,midg; igrid,midg,midg 8.7820385E-03 5.9647807E-03 gauss-seidel spectral radius is 0.9984422 estimated iterations to convergence 201 setup time was (sec) 0.8900000 now iterating at: 10:25:04 rms-change max change #iterations 3.595532 170.5472 at 10iterations 1.597726 56.05874 at 20iterations 0.7069762 26.30210 at 30iterations 0.3120517 11.63993 at 40iterations 0.1385622 5.075382 at 50iterations 6.1354071E-02 2.023420 at 60iterations 2.7037648E-02 0.9037490 at 70iterations 1.2036151E-02 0.4926996 at 80iterations 5.3436919E-03 0.1813889 at 90iterations 2.3741445E-03 0.1017723 at 100iterations 1.0517135E-03 3.6653996E-02 at 110iterations 4.6649997E-04 1.7518044E-02 at 120iterations finished qdiffx linear iterations at : 10:25:13 total time elapsed so far: 10.42000 # loops : 120 mean,max change (kT/e) : 4.6649997E-04 1.7518044E-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) 10.59000 DelPhi exited at 10:25:14 10.595u 0.424s 0:11.42 96.4% 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 Mon Oct 10 2011 at 10:25:14 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2626 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: 2.645704 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): -17.80700 31.80100 ymin,ymax (A): -60.05300 -2.845000 zmin,zma (A): -0.4200000 60.13100 x,y,z range (A): 49.60800 57.20800 60.55100 scale (grids/A): 2.645704 object centre (A): 6.997000 -31.44900 29.85550 number of atom coordinates read : 2626 total number of charged atoms : 2481 net assigned charge : 9.000021 assigned positive charge : 385.2632 centred at (gu) : 83.56245 83.25155 79.68750 assigned negative charge : -376.2636 centred at (gu) : 83.76814 82.49229 79.54462 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29664 grid for indexing accessible points = 1.400000 m= 70097 mr = 99735 m= 23179 mr = 51926 m= 4485 mr = 16309 m= 404 mr = 2550 m= 11 mr = 132 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 81440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19842 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) : 1.763802 object centre at (A) : 6.997000 -31.44900 29.85550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3840528 5.0749458E-02 midg,1,midg; midg,igrid,midg 0.3064860 0.4006948 1,midg,midg; igrid,midg,midg 1.5292669E-02 5.0646551E-02 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 1.760000 now iterating at: 10:25:16 rms-change max change #iterations 9.164618 309.8625 at 10iterations 5.467092 146.6627 at 20iterations 3.205393 79.16756 at 30iterations 1.871020 49.35206 at 40iterations 1.082347 26.91437 at 50iterations 0.6252058 16.10566 at 60iterations 0.3594758 8.263668 at 70iterations 0.2061925 5.083630 at 80iterations 0.1179876 3.330576 at 90iterations 6.7525163E-02 1.458415 at 100iterations 3.8620960E-02 0.8393202 at 110iterations 2.2027941E-02 0.4660935 at 120iterations 1.2569868E-02 0.2935791 at 130iterations 7.1456158E-03 0.1532555 at 140iterations 4.0780474E-03 8.4892273E-02 at 150iterations 2.3164998E-03 4.8095703E-02 at 160iterations 1.3192937E-03 2.6876450E-02 at 170iterations 7.5079477E-04 1.7999649E-02 at 180iterations finished qdiffx linear iterations at : 10:25:32 total time elapsed so far: 17.97000 # loops : 180 mean,max change (kT/e) : 7.5079477E-04 1.7999649E-02 energy calculations done at 17.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.14000 DelPhi exited at 10:25:33 18.145u 0.464s 0:18.92 98.3% 0+0k 0+0io 0pf+0w