Tue Oct 11 08:29:13 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 Tue Oct 11 2011 at 08:29:13 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 !!! WARNING: HIR 79 has a net charge of 0.5140 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: 0.6585276 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): -10.30600 37.18300 ymin,ymax (A): -26.62900 21.58900 zmin,zma (A): -8.081000 45.97900 x,y,z range (A): 47.48900 48.21800 54.06000 scale (grids/A): 0.6585276 object centre (A): 13.43850 -2.520000 18.94900 number of atom coordinates read : 2820 total number of charged atoms : 2670 net assigned charge : 0.5140191 assigned positive charge : 430.9746 centred at (gu) : 89.40897 90.39855 91.42643 assigned negative charge : -430.4612 centred at (gu) : 89.11309 90.29604 91.38509 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8229 nv = 96 ne = 84 npr = 57502 no. pairs analyzed = 57502 no. exposed pairs = 3386 no. arc points = 23214 no. surface atoms = 1135 nbur = 1685 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4787 m= 6 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.3300000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3149551E-09 1.3853580E-08 midg,1,midg; midg,igrid,midg -1.8641865E-08 2.4943731E-08 1,midg,midg; igrid,midg,midg -7.1301486E-08 5.4703825E-08 gauss-seidel spectral radius is 0.9880653 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 08:29:14 rms-change max change #iterations 0.1812045 23.41366 at 10iterations 1.9059185E-02 2.481882 at 20iterations 2.0328115E-03 0.2513103 at 30iterations 2.3723168E-04 2.9846191E-02 at 40iterations 3.6781970E-05 6.4215660E-03 at 50iterations finished qdiffx linear iterations at : 08:29:16 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.6781970E-05 6.4215660E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:29:17 3.498u 0.185s 0:04.05 90.6% 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 Oct 11 2011 at 08:29:17 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 !!! WARNING: HIR 79 has a net charge of 0.5140 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: 1.975583 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): -10.30600 37.18300 ymin,ymax (A): -26.62900 21.58900 zmin,zma (A): -8.081000 45.97900 x,y,z range (A): 47.48900 48.21800 54.06000 scale (grids/A): 1.975583 object centre (A): 13.43850 -2.520000 18.94900 number of atom coordinates read : 2820 total number of charged atoms : 2670 net assigned charge : 0.5140191 assigned positive charge : 430.9746 centred at (gu) : 88.22655 91.19508 94.27867 assigned negative charge : -430.4612 centred at (gu) : 87.33913 90.88771 94.15502 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87318 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23214 grid for indexing accessible points = 1.400000 m= 36143 mr = 62218 m= 6877 mr = 27980 m= 508 mr = 4772 m= 14 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 3352 time to turn everything in is 0.6600000 number of dielectric boundary points 35667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21065 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) : 0.6585276 object centre at (A) : 13.43850 -2.520000 18.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1418605E-02 5.1139169E-03 midg,1,midg; midg,igrid,midg -1.4147339E-02 2.7404200E-02 1,midg,midg; igrid,midg,midg -2.6462508E-02 6.3453443E-02 gauss-seidel spectral radius is 0.9987484 estimated iterations to convergence 224 setup time was (sec) 0.9500000 now iterating at: 08:29:18 rms-change max change #iterations 4.860746 193.8869 at 10iterations 2.346009 79.68378 at 20iterations 1.137209 32.93436 at 30iterations 0.5512841 15.55937 at 40iterations 0.2669020 7.703586 at 50iterations 0.1292973 3.826145 at 60iterations 6.2731132E-02 1.708315 at 70iterations 3.0338295E-02 0.8719363 at 80iterations 1.4695291E-02 0.4074059 at 90iterations 7.1263821E-03 0.2009468 at 100iterations 3.4618564E-03 0.1008363 at 110iterations 1.6770164E-03 4.7376633E-02 at 120iterations finished qdiffx linear iterations at : 08:29:26 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.6770164E-03 4.7376633E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 08:29:27 9.474u 0.200s 0:09.95 97.1% 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 Oct 11 2011 at 08:29:27 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 !!! WARNING: HIR 79 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.963374 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): -10.30600 37.18300 ymin,ymax (A): -26.62900 21.58900 zmin,zma (A): -8.081000 45.97900 x,y,z range (A): 47.48900 48.21800 54.06000 scale (grids/A): 2.963374 object centre (A): 13.43850 -2.520000 18.94900 number of atom coordinates read : 2820 total number of charged atoms : 2670 net assigned charge : 0.5140191 assigned positive charge : 430.9746 centred at (gu) : 87.33961 91.79243 96.41795 assigned negative charge : -430.4612 centred at (gu) : 86.00852 91.33167 96.23257 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 201135 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23214 grid for indexing accessible points = 1.400000 m= 111216 mr = 149600 m= 46710 mr = 93314 m= 12970 mr = 39279 m= 2175 mr = 10201 m= 162 mr = 1571 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 11595 time to turn everything in is 1.740000 number of dielectric boundary points 80323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 21360 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) : 1.975583 object centre at (A) : 13.43850 -2.520000 18.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5272616 0.2705431 midg,1,midg; midg,igrid,midg -0.1605391 0.3175864 1,midg,midg; igrid,midg,midg -7.8800574E-02 0.5501267 gauss-seidel spectral radius is 0.9992871 estimated iterations to convergence 296 setup time was (sec) 2.060000 now iterating at: 08:29:29 rms-change max change #iterations 11.14957 398.1877 at 10iterations 6.566422 179.8307 at 20iterations 3.868559 90.52225 at 30iterations 2.271280 52.34119 at 40iterations 1.333913 25.49880 at 50iterations 0.7786931 14.83090 at 60iterations 0.4553941 8.082144 at 70iterations 0.2661107 4.764584 at 80iterations 0.1551762 2.849697 at 90iterations 9.0319097E-02 1.483014 at 100iterations 5.2709725E-02 0.8084879 at 110iterations 3.0675063E-02 0.5372324 at 120iterations 1.7853713E-02 0.2921448 at 130iterations 1.0372873E-02 0.1742306 at 140iterations 6.0518775E-03 0.1035080 at 150iterations 3.5216713E-03 5.9024811E-02 at 160iterations 2.0551747E-03 3.7503242E-02 at 170iterations 1.2015578E-03 2.0404816E-02 at 180iterations finished qdiffx linear iterations at : 08:29:40 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.2015578E-03 2.0404816E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 08:29:41 13.166u 0.221s 0:13.84 96.6% 0+0k 0+0io 0pf+0w