Mon Oct 10 14:07:48 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 14:07:48 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: 294 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 : 593.7391 centred at (gu) : 91.35053 91.04392 91.10090 assigned negative charge : -598.7418 centred at (gu) : 91.29822 91.15741 90.99654 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 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 0.4700000 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 0.5900000 number of grid points assigned charge 10632 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6669140E-09 2.1005087E-09 midg,1,midg; midg,igrid,midg 1.4043107E-09 -4.7324664E-09 1,midg,midg; igrid,midg,midg -1.5850188E-09 5.1964949E-10 gauss-seidel spectral radius is 0.9844092 estimated iterations to convergence 66 setup time was (sec) 0.7500000 now iterating at: 14:07:49 rms-change max change #iterations 0.1117511 17.18235 at 10iterations 9.0364888E-03 1.243588 at 20iterations 1.1571412E-03 0.1718674 at 30iterations 2.8063211E-04 4.4080734E-02 at 40iterations 8.2418272E-05 1.2359619E-02 at 50iterations finished qdiffx linear iterations at : 14:07:53 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 8.2418272E-05 1.2359619E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 14:07:54 4.340u 0.286s 0:05.77 80.0% 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 Mon Oct 10 2011 at 14:07:54 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: 294 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 : 593.7391 centred at (gu) : 94.05045 93.13066 93.30125 assigned negative charge : -598.7418 centred at (gu) : 93.89439 93.47202 92.98940 start vw surface at 0.2600000 fill in re-entrant regions at 0.4200000 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 = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 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 1.010000 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 -2.6752530E-02 -9.5574139E-03 midg,1,midg; midg,igrid,midg 3.0871389E-02 -1.8012216E-02 1,midg,midg; igrid,midg,midg 4.9107950E-03 -1.3790525E-02 gauss-seidel spectral radius is 0.9984609 estimated iterations to convergence 202 setup time was (sec) 1.180000 now iterating at: 14:07:56 rms-change max change #iterations 4.445460 159.0527 at 10iterations 1.984189 67.16383 at 20iterations 0.8829851 28.36340 at 30iterations 0.3940918 12.37537 at 40iterations 0.1768269 5.278708 at 50iterations 7.9400644E-02 2.319611 at 60iterations 3.5529558E-02 1.145996 at 70iterations 1.5963409E-02 0.5134103 at 80iterations 7.1940245E-03 0.2360725 at 90iterations 3.2737618E-03 0.1019173 at 100iterations 1.5095966E-03 5.0941467E-02 at 110iterations 7.1536464E-04 2.3952484E-02 at 120iterations finished qdiffx linear iterations at : 14:08:04 total time elapsed so far: 9.950000 # loops : 120 mean,max change (kT/e) : 7.1536464E-04 2.3952484E-02 energy calculations done at 9.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.13000 DelPhi exited at 14:08:05 10.131u 0.317s 0:11.01 94.8% 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 14:08:05 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: 294 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 : 593.7391 centred at (gu) : 96.07512 94.69580 94.95134 assigned negative charge : -598.7418 centred at (gu) : 95.84154 95.20798 94.48409 start vw surface at 0.1800000 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 = 1.240000 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 2.200000 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 -0.3465769 -0.2010101 midg,1,midg; midg,igrid,midg 0.4909669 -0.2730104 1,midg,midg; igrid,midg,midg 0.1645368 -0.2802215 gauss-seidel spectral radius is 0.9992408 estimated iterations to convergence 286 setup time was (sec) 2.380000 now iterating at: 14:08:08 rms-change max change #iterations 11.21584 309.6657 at 10iterations 6.633463 154.4913 at 20iterations 3.875942 108.2437 at 30iterations 2.259712 46.18086 at 40iterations 1.308398 26.55462 at 50iterations 0.7552674 12.79119 at 60iterations 0.4346728 7.692299 at 70iterations 0.2503755 6.029671 at 80iterations 0.1440261 2.798595 at 90iterations 8.2624294E-02 1.631065 at 100iterations 4.7420379E-02 0.8574791 at 110iterations 2.7155127E-02 0.5212537 at 120iterations 1.5538652E-02 0.2838755 at 130iterations 8.9134239E-03 0.1629254 at 140iterations 5.1135775E-03 9.2839956E-02 at 150iterations 2.9318172E-03 5.0725937E-02 at 160iterations 1.6924526E-03 3.0438423E-02 at 170iterations 9.8078605E-04 1.7145157E-02 at 180iterations finished qdiffx linear iterations at : 14:08:23 total time elapsed so far: 17.24000 # loops : 180 mean,max change (kT/e) : 9.8078605E-04 1.7145157E-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 14:08:24 17.428u 0.342s 0:18.38 96.6% 0+0k 0+0io 0pf+0w