Tue Nov 22 14:18:22 PST 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 Tue Nov 22 2011 at 14:18:26 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6068561 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 0.6068561 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000011 assigned positive charge : 283.9281 centred at (gu) : 89.91544 90.22837 90.24303 assigned negative charge : -278.9283 centred at (gu) : 89.91572 90.30664 90.37053 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4820 nv = 96 ne = 84 npr = 39598 no. pairs analyzed = 39598 no. exposed pairs = 2546 no. arc points = 18082 no. surface atoms = 869 nbur = 1065 mkacc time = 8.9999996E-02 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 = 1.456000 m= 216 mr = 2491 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1843 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4039165E-09 -1.5878853E-09 midg,1,midg; midg,igrid,midg 4.9476427E-09 1.3734675E-10 1,midg,midg; igrid,midg,midg 2.7533424E-09 2.6365579E-09 gauss-seidel spectral radius is 0.9858894 estimated iterations to convergence 69 setup time was (sec) 0.4500000 now iterating at: 14:18:29 rms-change max change #iterations 9.7591765E-02 19.68756 at 10iterations 8.6817481E-03 1.484946 at 20iterations 7.4398360E-04 0.1577644 at 30iterations 6.2389976E-05 1.1798859E-02 at 40iterations 5.4207794E-06 8.2778931E-04 at 50iterations finished qdiffx linear iterations at : 14:18:37 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 5.4207794E-06 8.2778931E-04 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 14:18:39 3.284u 0.147s 0:13.70 24.9% 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 Tue Nov 22 2011 at 14:18:41 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.820568 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 1.820568 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000011 assigned positive charge : 283.9281 centred at (gu) : 89.74638 90.68523 90.72919 assigned negative charge : -278.9283 centred at (gu) : 89.74725 90.92020 91.11197 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18082 grid for indexing accessible points = 1.400000 m= 17980 mr = 34763 m= 2301 mr = 12993 m= 83 mr = 1206 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 23496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14090 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) : 0.6068561 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4286259E-03 -7.6671568E-04 midg,1,midg; midg,igrid,midg 5.9929308E-03 1.9677547E-03 1,midg,midg; igrid,midg,midg 4.3720186E-02 3.3247277E-02 gauss-seidel spectral radius is 0.9984328 estimated iterations to convergence 200 setup time was (sec) 0.6700000 now iterating at: 14:18:45 rms-change max change #iterations 3.237622 180.6017 at 10iterations 1.425897 54.34206 at 20iterations 0.6349291 25.52510 at 30iterations 0.2798877 10.47916 at 40iterations 0.1239982 5.170920 at 50iterations 5.4805655E-02 2.164340 at 60iterations 2.4439119E-02 0.8733978 at 70iterations 1.0807437E-02 0.4373674 at 80iterations 4.7769211E-03 0.1792259 at 90iterations 2.1135255E-03 7.2294950E-02 at 100iterations 9.3771337E-04 4.4712067E-02 at 110iterations 4.1695952E-04 1.7574310E-02 at 120iterations finished qdiffx linear iterations at : 14:19:06 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 4.1695952E-04 1.7574310E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 14:19:07 7.373u 0.165s 0:27.10 27.7% 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 Tue Nov 22 2011 at 14:19:09 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.730852 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 2.730852 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000011 assigned positive charge : 283.9281 centred at (gu) : 89.61964 91.02774 91.09381 assigned negative charge : -278.9283 centred at (gu) : 89.62098 91.38029 91.66801 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 120279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18082 grid for indexing accessible points = 1.400000 m= 59048 mr = 84490 m= 19642 mr = 47605 m= 3722 mr = 15510 m= 309 mr = 2467 m= 10 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 52767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 14416 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) : 1.820568 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6959014E-02 2.5682153E-02 midg,1,midg; midg,igrid,midg 4.0924221E-02 4.8661839E-02 1,midg,midg; igrid,midg,midg 0.6120614 0.3584601 gauss-seidel spectral radius is 0.9991888 estimated iterations to convergence 277 setup time was (sec) 1.260000 now iterating at: 14:19:16 rms-change max change #iterations 7.821301 317.4961 at 10iterations 4.485489 119.7724 at 20iterations 2.549913 70.00452 at 30iterations 1.440258 34.03329 at 40iterations 0.8132890 19.06755 at 50iterations 0.4578136 10.55088 at 60iterations 0.2570238 5.574137 at 70iterations 0.1437747 3.126694 at 80iterations 8.0811940E-02 1.961487 at 90iterations 4.5275349E-02 1.073376 at 100iterations 2.5279673E-02 0.5702324 at 110iterations 1.4198286E-02 0.3145888 at 120iterations 7.9260347E-03 0.1885321 at 130iterations 4.4441065E-03 0.1112976 at 140iterations 2.4836578E-03 5.6344986E-02 at 150iterations 1.3880805E-03 3.1044006E-02 at 160iterations 7.7555014E-04 1.7158747E-02 at 170iterations 4.3365511E-04 9.4108582E-03 at 180iterations finished qdiffx linear iterations at : 14:19:53 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 4.3365511E-04 9.4108582E-03 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 14:19:55 13.730u 0.187s 0:46.01 30.2% 0+0k 0+0io 0pf+0w