Mon Oct 10 14:14:48 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+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 14:14:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2470 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5583701 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): -10.40300 53.35400 ymin,ymax (A): 91.26100 144.6360 zmin,zma (A): 22.60100 68.36200 x,y,z range (A): 63.75700 53.37500 45.76100 scale (grids/A): 0.5583701 object centre (A): 21.47550 117.9485 45.48150 number of atom coordinates read : 2470 total number of charged atoms : 2321 net assigned charge : -0.4999908 assigned positive charge : 356.9441 centred at (gu) : 89.90374 89.14581 89.80771 assigned negative charge : -357.4448 centred at (gu) : 89.90237 89.19553 89.71280 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5199 nv = 96 ne = 84 npr = 47847 no. pairs analyzed = 47847 no. exposed pairs = 3473 no. arc points = 24957 no. surface atoms = 1153 nbur = 1317 mkacc time = 0.1600000 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 = 1.540000 m= 244 mr = 2518 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2413 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0077956E-10 7.0254375E-10 midg,1,midg; midg,igrid,midg 4.4999743E-10 -3.8337683E-10 1,midg,midg; igrid,midg,midg -6.4766595E-11 -3.9457316E-11 gauss-seidel spectral radius is 0.9834263 estimated iterations to convergence 64 setup time was (sec) 0.6500000 now iterating at: 14:14:49 rms-change max change #iterations 6.8880893E-02 13.63384 at 10iterations 4.8970194E-03 0.9221950 at 20iterations 3.4698818E-04 6.0651779E-02 at 30iterations 2.5064775E-05 4.2114258E-03 at 40iterations 1.9183985E-06 3.1280518E-04 at 50iterations finished qdiffx linear iterations at : 14:14:53 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 1.9183985E-06 3.1280518E-04 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 14:14:54 4.466u 0.411s 0:05.29 92.0% 0+0k 0+0io 5pf+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 14:14:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2470 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.675110 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): -10.40300 53.35400 ymin,ymax (A): 91.26100 144.6360 zmin,zma (A): 22.60100 68.36200 x,y,z range (A): 63.75700 53.37500 45.76100 scale (grids/A): 1.675110 object centre (A): 21.47550 117.9485 45.48150 number of atom coordinates read : 2470 total number of charged atoms : 2321 net assigned charge : -0.4999908 assigned positive charge : 356.9441 centred at (gu) : 89.71066 87.43701 89.42252 assigned negative charge : -357.4448 centred at (gu) : 89.70695 87.58624 89.13818 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24957 grid for indexing accessible points = 1.400000 m= 18343 mr = 36047 m= 2329 mr = 12753 m= 74 mr = 1191 m= 0 mr = 9 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 27012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17870 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) : 0.5583701 object centre at (A) : 21.47550 117.9485 45.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4128809E-03 4.7169216E-03 midg,1,midg; midg,igrid,midg -3.6641185E-03 -7.1029556E-03 1,midg,midg; igrid,midg,midg -9.3261385E-03 1.7961349E-02 gauss-seidel spectral radius is 0.9982386 estimated iterations to convergence 189 setup time was (sec) 0.9400000 now iterating at: 14:14:55 rms-change max change #iterations 3.065763 139.3774 at 10iterations 1.289387 55.00209 at 20iterations 0.5448744 21.24712 at 30iterations 0.2293656 9.440195 at 40iterations 9.6377552E-02 3.577492 at 50iterations 4.0586755E-02 1.608865 at 60iterations 1.7239962E-02 0.6785927 at 70iterations 7.2221565E-03 0.2753372 at 80iterations 3.0692571E-03 0.1324413 at 90iterations 1.2951313E-03 4.7331810E-02 at 100iterations 5.4503599E-04 1.9966125E-02 at 110iterations 2.3185603E-04 1.0536194E-02 at 120iterations finished qdiffx linear iterations at : 14:15:05 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 2.3185603E-04 1.0536194E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 14:15:05 10.631u 0.444s 0:11.41 97.0% 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 14:15:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2470 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.512665 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): -10.40300 53.35400 ymin,ymax (A): 91.26100 144.6360 zmin,zma (A): 22.60100 68.36200 x,y,z range (A): 63.75700 53.37500 45.76100 scale (grids/A): 2.512665 object centre (A): 21.47550 117.9485 45.48150 number of atom coordinates read : 2470 total number of charged atoms : 2321 net assigned charge : -0.4999908 assigned positive charge : 356.9441 centred at (gu) : 89.56595 86.15532 89.13374 assigned negative charge : -357.4448 centred at (gu) : 89.56036 86.37939 88.70725 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 130281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24957 grid for indexing accessible points = 1.400000 m= 61058 mr = 88773 m= 19962 mr = 47683 m= 3780 mr = 15244 m= 341 mr = 2571 m= 3 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 60992 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 18555 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) : 1.675110 object centre at (A) : 21.47550 117.9485 45.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2285381E-02 7.5413994E-02 midg,1,midg; midg,igrid,midg -7.1634121E-02 -7.4484490E-02 1,midg,midg; igrid,midg,midg -0.1196025 0.5682017 gauss-seidel spectral radius is 0.9991522 estimated iterations to convergence 271 setup time was (sec) 1.860000 now iterating at: 14:15:08 rms-change max change #iterations 8.080733 355.3082 at 10iterations 4.616087 159.2135 at 20iterations 2.607201 68.25562 at 30iterations 1.469803 39.20628 at 40iterations 0.8225158 20.77084 at 50iterations 0.4598863 10.48581 at 60iterations 0.2561207 5.981385 at 70iterations 0.1428260 3.147017 at 80iterations 7.9133645E-02 1.882376 at 90iterations 4.3819182E-02 1.104423 at 100iterations 2.4269868E-02 0.5407829 at 110iterations 1.3438529E-02 0.2982917 at 120iterations 7.4489606E-03 0.1601257 at 130iterations 4.1130884E-03 9.0310574E-02 at 140iterations 2.2727698E-03 5.3992748E-02 at 150iterations 1.2561833E-03 2.9193878E-02 at 160iterations 6.9280493E-04 1.5232086E-02 at 170iterations 3.8183754E-04 9.4223022E-03 at 180iterations finished qdiffx linear iterations at : 14:15:26 total time elapsed so far: 20.19000 # loops : 180 mean,max change (kT/e) : 3.8183754E-04 9.4223022E-03 energy calculations done at 20.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.41000 DelPhi exited at 14:15:26 20.410u 0.486s 0:21.24 98.3% 0+0k 0+0io 0pf+0w