Sun Oct 9 17:12:00 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 Sun Oct 9 2011 at 17:12:00 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4671 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5879730 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): 2.923000 61.76500 ymin,ymax (A): -8.835000 51.71200 zmin,zma (A): -1.957000 57.47600 x,y,z range (A): 58.84200 60.54700 59.43300 scale (grids/A): 0.5879730 object centre (A): 32.34400 21.43850 27.75950 number of atom coordinates read : 4671 total number of charged atoms : 4557 net assigned charge : -0.3789496 assigned positive charge : 720.3927 centred at (gu) : 88.77425 89.49153 90.18941 assigned negative charge : -720.7767 centred at (gu) : 88.68697 89.51864 90.14587 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10737 nv = 96 ne = 84 npr = 93901 no. pairs analyzed = 93901 no. exposed pairs = 5501 no. arc points = 37192 no. surface atoms = 1886 nbur = 2785 mkacc time = 0.2300000 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= 519 mr = 6197 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 5010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3884 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 13842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9973312E-09 2.0296396E-09 midg,1,midg; midg,igrid,midg 1.3387109E-09 -1.1730960E-09 1,midg,midg; igrid,midg,midg -5.5398588E-09 2.9519724E-09 gauss-seidel spectral radius is 0.9851971 estimated iterations to convergence 67 setup time was (sec) 0.7200000 now iterating at: 17:12:01 rms-change max change #iterations 0.1412289 15.89591 at 10iterations 1.3266929E-02 1.725899 at 20iterations 2.9428266E-03 0.3117981 at 30iterations 1.2475977E-03 0.1324702 at 40iterations 5.7252817E-04 6.6185236E-02 at 50iterations finished qdiffx linear iterations at : 17:12:04 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 5.7252817E-04 6.6185236E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:12:05 3.599u 0.135s 0:04.11 90.5% 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 Sun Oct 9 2011 at 17:12:05 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4671 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.763919 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): 2.923000 61.76500 ymin,ymax (A): -8.835000 51.71200 zmin,zma (A): -1.957000 57.47600 x,y,z range (A): 58.84200 60.54700 59.43300 scale (grids/A): 1.763919 object centre (A): 32.34400 21.43850 27.75950 number of atom coordinates read : 4671 total number of charged atoms : 4557 net assigned charge : -0.3789496 assigned positive charge : 720.3927 centred at (gu) : 86.32142 88.47346 90.56700 assigned negative charge : -720.7767 centred at (gu) : 86.06056 88.55618 90.43734 start vw surface at 0.2100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 118316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37192 grid for indexing accessible points = 1.400000 m= 43270 mr = 86311 m= 6143 mr = 31704 m= 267 mr = 3553 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.8400000 number of dielectric boundary points 46350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 35427 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) : 0.5879730 object centre at (A) : 32.34400 21.43850 27.75950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6645834E-02 -1.8039997E-03 midg,1,midg; midg,igrid,midg 1.4840837E-02 1.3055049E-02 1,midg,midg; igrid,midg,midg -4.1608959E-03 1.4336492E-02 gauss-seidel spectral radius is 0.9986036 estimated iterations to convergence 212 setup time was (sec) 1.130000 now iterating at: 17:12:06 rms-change max change #iterations 5.235515 177.6513 at 10iterations 2.432703 65.30077 at 20iterations 1.130858 31.08994 at 30iterations 0.5266796 13.96800 at 40iterations 0.2455971 6.920837 at 50iterations 0.1144884 3.440109 at 60iterations 5.3714428E-02 1.497059 at 70iterations 2.5513111E-02 0.6554157 at 80iterations 1.2366551E-02 0.3329506 at 90iterations 6.3515436E-03 0.1641598 at 100iterations 3.6068258E-03 9.8870158E-02 at 110iterations 2.2993176E-03 6.4948082E-02 at 120iterations finished qdiffx linear iterations at : 17:12:13 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.2993176E-03 6.4948082E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 17:12:13 7.992u 0.193s 0:08.52 96.0% 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 Sun Oct 9 2011 at 17:12:13 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4671 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.645879 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): 2.923000 61.76500 ymin,ymax (A): -8.835000 51.71200 zmin,zma (A): -1.957000 57.47600 x,y,z range (A): 58.84200 60.54700 59.43300 scale (grids/A): 2.645879 object centre (A): 32.34400 21.43850 27.75950 number of atom coordinates read : 4671 total number of charged atoms : 4557 net assigned charge : -0.3789496 assigned positive charge : 720.3927 centred at (gu) : 84.48152 87.70963 90.85003 assigned negative charge : -720.7767 centred at (gu) : 84.09086 87.83411 90.65611 start vw surface at 0.2000000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 274388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37192 grid for indexing accessible points = 1.400000 m= 141936 mr = 208777 m= 49062 mr = 116968 m= 10687 mr = 38734 m= 1244 mr = 7634 m= 54 mr = 757 m= 0 mr = 12 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 801 time to turn everything in is 2.150000 number of dielectric boundary points 104489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 36443 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) : 1.763919 object centre at (A) : 32.34400 21.43850 27.75950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3867981 0.2586970 midg,1,midg; midg,igrid,midg -0.1565217 -7.6720856E-02 1,midg,midg; igrid,midg,midg 4.7333591E-02 0.2960466 gauss-seidel spectral radius is 0.9992946 estimated iterations to convergence 297 setup time was (sec) 2.470000 now iterating at: 17:12:16 rms-change max change #iterations 12.81047 394.4238 at 10iterations 7.683661 151.7510 at 20iterations 4.589194 75.27916 at 30iterations 2.714850 49.38713 at 40iterations 1.604375 27.90241 at 50iterations 0.9464323 15.34238 at 60iterations 0.5553531 8.597435 at 70iterations 0.3256673 4.981946 at 80iterations 0.1912203 3.058649 at 90iterations 0.1120269 1.840904 at 100iterations 6.5637156E-02 0.9594231 at 110iterations 3.8516659E-02 0.5903301 at 120iterations 2.2642955E-02 0.3709278 at 130iterations 1.3380666E-02 0.1918042 at 140iterations 8.0058388E-03 0.1232548 at 150iterations 4.9084313E-03 9.0543628E-02 at 160iterations 3.1365335E-03 4.7082901E-02 at 170iterations 2.1222939E-03 3.4805298E-02 at 180iterations finished qdiffx linear iterations at : 17:12:27 total time elapsed so far: 13.25000 # loops : 180 mean,max change (kT/e) : 2.1222939E-03 3.4805298E-02 energy calculations done at 13.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 17:12:27 13.434u 0.181s 0:13.89 97.9% 0+0k 0+0io 0pf+0w