Mon Oct 10 19:43:55 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 19:43:55 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 = 3726 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: 0.5420549 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): 7.2000027E-02 65.74800 ymin,ymax (A): -8.736000 38.58000 zmin,zma (A): -19.82600 41.12500 x,y,z range (A): 65.67600 47.31600 60.95100 scale (grids/A): 0.5420549 object centre (A): 32.91000 14.92200 10.64950 number of atom coordinates read : 3726 total number of charged atoms : 3563 net assigned charge : -11.99995 assigned positive charge : 553.0250 centred at (gu) : 88.82028 89.67214 90.73409 assigned negative charge : -565.0267 centred at (gu) : 88.82843 89.72905 90.83366 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6984 nv = 96 ne = 84 npr = 77522 no. pairs analyzed = 77522 no. exposed pairs = 4488 no. arc points = 30107 no. surface atoms = 1522 nbur = 2204 mkacc time = 0.1400000 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 = 1.568000 m= 301 mr = 3811 m= 0 mr = 20 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3027 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2138815E-11 -1.6425401E-09 midg,1,midg; midg,igrid,midg -2.4069652E-10 -9.7005326E-10 1,midg,midg; igrid,midg,midg -7.6584145E-10 -5.2227500E-10 gauss-seidel spectral radius is 0.9825075 estimated iterations to convergence 62 setup time was (sec) 0.4400000 now iterating at: 19:43:55 rms-change max change #iterations 8.3369039E-02 12.89475 at 10iterations 7.3064296E-03 1.409691 at 20iterations 1.2873717E-03 0.1543312 at 30iterations 3.5324076E-04 4.8837662E-02 at 40iterations 1.0408658E-04 1.5195847E-02 at 50iterations finished qdiffx linear iterations at : 19:43:58 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.0408658E-04 1.5195847E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 19:43:59 3.483u 0.185s 0:04.34 84.3% 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 19:43:59 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 = 3726 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: 1.626165 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): 7.2000027E-02 65.74800 ymin,ymax (A): -8.736000 38.58000 zmin,zma (A): -19.82600 41.12500 x,y,z range (A): 65.67600 47.31600 60.95100 scale (grids/A): 1.626165 object centre (A): 32.91000 14.92200 10.64950 number of atom coordinates read : 3726 total number of charged atoms : 3563 net assigned charge : -11.99995 assigned positive charge : 553.0250 centred at (gu) : 86.45992 89.01566 92.20120 assigned negative charge : -565.0267 centred at (gu) : 86.48494 89.18675 92.50066 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 78693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25210 mr = 55719 m= 2689 mr = 17697 m= 84 mr = 1359 m= 0 mr = 3 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.3900000 number of dielectric boundary points 31898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 27275 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) : 0.5420549 object centre at (A) : 32.91000 14.92200 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3447769E-03 -2.8528124E-02 midg,1,midg; midg,igrid,midg -1.1036416E-02 -1.3084815E-02 1,midg,midg; igrid,midg,midg -5.3875623E-03 -8.1842104E-03 gauss-seidel spectral radius is 0.9982388 estimated iterations to convergence 189 setup time was (sec) 0.5900000 now iterating at: 19:44:00 rms-change max change #iterations 3.739977 155.2125 at 10iterations 1.584798 57.63620 at 20iterations 0.6716164 22.73140 at 30iterations 0.2854629 10.61447 at 40iterations 0.1208210 4.048506 at 50iterations 5.1495351E-02 1.714737 at 60iterations 2.1955799E-02 0.7517776 at 70iterations 9.5302369E-03 0.3258405 at 80iterations 4.2061913E-03 0.1260109 at 90iterations 1.9541797E-03 6.5389633E-02 at 100iterations 9.8071340E-04 3.3859253E-02 at 110iterations 5.3972268E-04 1.7465591E-02 at 120iterations finished qdiffx linear iterations at : 19:44:07 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 5.3972268E-04 1.7465591E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 19:44:07 7.852u 0.225s 0:08.41 95.9% 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 19:44:07 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 = 3726 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: 2.439247 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): 7.2000027E-02 65.74800 ymin,ymax (A): -8.736000 38.58000 zmin,zma (A): -19.82600 41.12500 x,y,z range (A): 65.67600 47.31600 60.95100 scale (grids/A): 2.439247 object centre (A): 32.91000 14.92200 10.64950 number of atom coordinates read : 3726 total number of charged atoms : 3563 net assigned charge : -11.99995 assigned positive charge : 553.0250 centred at (gu) : 84.68933 88.52304 93.30132 assigned negative charge : -565.0267 centred at (gu) : 84.72736 88.78006 93.75076 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 183206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 87545 mr = 136294 m= 25128 mr = 70262 m= 4355 mr = 18950 m= 328 mr = 2822 m= 2 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 800 time to turn everything in is 0.9500000 number of dielectric boundary points 72080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 28464 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) : 1.626165 object centre at (A) : 32.91000 14.92200 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3853713 -0.4540501 midg,1,midg; midg,igrid,midg -0.1787905 -0.1777591 1,midg,midg; igrid,midg,midg 2.1698652E-02 -0.4008153 gauss-seidel spectral radius is 0.9991671 estimated iterations to convergence 274 setup time was (sec) 1.190000 now iterating at: 19:44:09 rms-change max change #iterations 9.720521 295.0382 at 10iterations 5.518987 136.7774 at 20iterations 3.121145 65.66068 at 30iterations 1.753556 37.98518 at 40iterations 0.9850890 21.04581 at 50iterations 0.5509858 10.23494 at 60iterations 0.3084849 5.801735 at 70iterations 0.1722990 3.144365 at 80iterations 9.6228167E-02 1.919110 at 90iterations 5.3832974E-02 1.127537 at 100iterations 3.0083973E-02 0.5725636 at 110iterations 1.6913073E-02 0.3249197 at 120iterations 9.5451837E-03 0.1822128 at 130iterations 5.4595903E-03 0.1051207 at 140iterations 3.1850259E-03 5.8557510E-02 at 150iterations 1.9229093E-03 3.8402557E-02 at 160iterations 1.2103746E-03 2.2920609E-02 at 170iterations 8.0058770E-04 1.5567780E-02 at 180iterations finished qdiffx linear iterations at : 19:44:20 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 8.0058770E-04 1.5567780E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 19:44:21 12.671u 0.209s 0:13.31 96.6% 0+0k 0+0io 0pf+0w