Mon Oct 10 14:07:13 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+sph.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 Mon Oct 10 2011 at 14:07:13 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3826 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5740917 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): -4.794000 55.83200 ymin,ymax (A): -25.46900 36.54200 zmin,zma (A): -10.43500 42.22900 x,y,z range (A): 60.62600 62.01100 52.66400 scale (grids/A): 0.5740917 object centre (A): 25.51900 5.536500 15.89700 number of atom coordinates read : 3826 total number of charged atoms : 3682 net assigned charge : -4.999992 assigned positive charge : 592.9390 centred at (gu) : 91.35381 91.05116 91.10354 assigned negative charge : -597.9418 centred at (gu) : 91.30257 91.16451 91.00050 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8255 nv = 96 ne = 84 npr = 78035 no. pairs analyzed = 78035 no. exposed pairs = 4844 no. arc points = 33268 no. surface atoms = 1640 nbur = 2186 mkacc time = 0.2200000 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= 340 mr = 4391 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3366 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10632 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6365670E-09 2.0575568E-09 midg,1,midg; midg,igrid,midg 1.3971428E-09 -4.7303041E-09 1,midg,midg; igrid,midg,midg -1.5628582E-09 4.8319132E-10 gauss-seidel spectral radius is 0.9844092 estimated iterations to convergence 66 setup time was (sec) 0.7300000 now iterating at: 14:07:15 rms-change max change #iterations 0.1113087 17.18235 at 10iterations 8.9087421E-03 1.226665 at 20iterations 1.0941894E-03 0.1630363 at 30iterations 2.5781462E-04 4.0487289E-02 at 40iterations 7.5196629E-05 1.1339188E-02 at 50iterations finished qdiffx linear iterations at : 14:07:18 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 7.5196629E-05 1.1339188E-02 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 14:07:19 4.292u 0.305s 0:05.09 90.1% 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 14:07:19 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3826 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.722275 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): -4.794000 55.83200 ymin,ymax (A): -25.46900 36.54200 zmin,zma (A): -10.43500 42.22900 x,y,z range (A): 60.62600 62.01100 52.66400 scale (grids/A): 1.722275 object centre (A): 25.51900 5.536500 15.89700 number of atom coordinates read : 3826 total number of charged atoms : 3682 net assigned charge : -4.999992 assigned positive charge : 592.9390 centred at (gu) : 94.06032 93.15237 93.30915 assigned negative charge : -597.9418 centred at (gu) : 93.90745 93.49326 93.00123 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 91036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33268 grid for indexing accessible points = 1.400000 m= 30061 mr = 63251 m= 3514 mr = 20517 m= 119 mr = 1746 m= 0 mr = 15 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 39201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 28539 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) : 0.5740917 object centre at (A) : 25.51900 5.536500 15.89700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6609858E-02 -9.7170975E-03 midg,1,midg; midg,igrid,midg 3.0682292E-02 -1.8057968E-02 1,midg,midg; igrid,midg,midg 5.0282525E-03 -1.3916919E-02 gauss-seidel spectral radius is 0.9984609 estimated iterations to convergence 202 setup time was (sec) 1.120000 now iterating at: 14:07:20 rms-change max change #iterations 4.437524 159.0527 at 10iterations 1.980628 67.16383 at 20iterations 0.8812494 28.55028 at 30iterations 0.3933520 12.37524 at 40iterations 0.1764878 5.301928 at 50iterations 7.9220384E-02 2.307251 at 60iterations 3.5436299E-02 1.146225 at 70iterations 1.5917175E-02 0.5148726 at 80iterations 7.1630878E-03 0.2313232 at 90iterations 3.2514518E-03 9.9575043E-02 at 100iterations 1.4922728E-03 5.0258636E-02 at 110iterations 7.0072041E-04 2.3445129E-02 at 120iterations finished qdiffx linear iterations at : 14:07:29 total time elapsed so far: 9.890000 # loops : 120 mean,max change (kT/e) : 7.0072041E-04 2.3445129E-02 energy calculations done at 9.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 14:07:30 10.071u 0.319s 0:10.99 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 Mon Oct 10 2011 at 14:07:30 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3826 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.583413 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): -4.794000 55.83200 ymin,ymax (A): -25.46900 36.54200 zmin,zma (A): -10.43500 42.22900 x,y,z range (A): 60.62600 62.01100 52.66400 scale (grids/A): 2.583413 object centre (A): 25.51900 5.536500 15.89700 number of atom coordinates read : 3826 total number of charged atoms : 3682 net assigned charge : -4.999992 assigned positive charge : 592.9390 centred at (gu) : 96.08991 94.72836 94.96320 assigned negative charge : -597.9418 centred at (gu) : 95.86111 95.23985 94.50184 start vw surface at 0.1900000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 211608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33268 grid for indexing accessible points = 1.400000 m= 102043 mr = 154657 m= 31034 mr = 80879 m= 5765 mr = 22987 m= 484 mr = 3790 m= 11 mr = 237 m= 0 mr = 2 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 88393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 29443 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) : 1.722275 object centre at (A) : 25.51900 5.536500 15.89700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3448830 -0.2029363 midg,1,midg; midg,igrid,midg 0.4881356 -0.2737323 1,midg,midg; igrid,midg,midg 0.1659510 -0.2818984 gauss-seidel spectral radius is 0.9992408 estimated iterations to convergence 286 setup time was (sec) 2.360000 now iterating at: 14:07:32 rms-change max change #iterations 11.19721 309.6705 at 10iterations 6.623414 154.4951 at 20iterations 3.870177 108.1928 at 30iterations 2.256616 45.23850 at 40iterations 1.306602 26.67482 at 50iterations 0.7541779 12.87991 at 60iterations 0.4341199 7.753056 at 70iterations 0.2500489 6.028458 at 80iterations 0.1438403 2.803841 at 90iterations 8.2515374E-02 1.646921 at 100iterations 4.7357835E-02 0.8525887 at 110iterations 2.7114399E-02 0.5174887 at 120iterations 1.5514358E-02 0.2857921 at 130iterations 8.8948403E-03 0.1619018 at 140iterations 5.0999024E-03 9.3719244E-02 at 150iterations 2.9205473E-03 5.0880432E-02 at 160iterations 1.6824724E-03 3.0114174E-02 at 170iterations 9.7106205E-04 1.6635895E-02 at 180iterations finished qdiffx linear iterations at : 14:07:47 total time elapsed so far: 17.24000 # loops : 180 mean,max change (kT/e) : 9.7106205E-04 1.6635895E-02 energy calculations done at 17.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.43000 DelPhi exited at 14:07:48 17.427u 0.345s 0:18.34 96.8% 0+0k 0+0io 0pf+0w