Tue Oct 11 03:15:24 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 03:15:25 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 = 3130 !!! WARNING: GLM 12 has a net charge of -0.0940 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: 0.5966847 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): -0.9230000 46.41500 ymin,ymax (A): 77.04600 136.7090 zmin,zma (A): 102.2550 161.1480 x,y,z range (A): 47.33800 59.66300 58.89300 scale (grids/A): 0.5966847 object centre (A): 22.74600 106.8775 131.7015 number of atom coordinates read : 3130 total number of charged atoms : 2987 net assigned charge : -7.093976 assigned positive charge : 467.1620 centred at (gu) : 90.61266 91.46606 91.78522 assigned negative charge : -474.2569 centred at (gu) : 90.54431 91.45405 91.78156 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7217 nv = 96 ne = 84 npr = 65473 no. pairs analyzed = 65473 no. exposed pairs = 3837 no. arc points = 26555 no. surface atoms = 1304 nbur = 1826 mkacc time = 0.1800000 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= 328 mr = 3919 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2697 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9174 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9508193E-09 -3.8555470E-09 midg,1,midg; midg,igrid,midg -2.3295095E-09 -3.1187417E-09 1,midg,midg; igrid,midg,midg -4.7816195E-09 -1.0177232E-11 gauss-seidel spectral radius is 0.9855049 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 03:15:25 rms-change max change #iterations 0.1172414 19.69903 at 10iterations 9.8571917E-03 1.372864 at 20iterations 9.2447578E-04 0.1393959 at 30iterations 1.3706009E-04 2.2194743E-02 at 40iterations 3.4032961E-05 6.3848495E-03 at 50iterations finished qdiffx linear iterations at : 03:15:29 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 3.4032961E-05 6.3848495E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 03:15:29 4.008u 0.258s 0:04.69 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 03:15:29 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 = 3130 !!! WARNING: GLM 12 has a net charge of -0.0940 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: 1.790054 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): -0.9230000 46.41500 ymin,ymax (A): 77.04600 136.7090 zmin,zma (A): 102.2550 161.1480 x,y,z range (A): 47.33800 59.66300 58.89300 scale (grids/A): 1.790054 object centre (A): 22.74600 106.8775 131.7015 number of atom coordinates read : 3130 total number of charged atoms : 2987 net assigned charge : -7.093976 assigned positive charge : 467.1620 centred at (gu) : 91.83723 94.39729 95.35447 assigned negative charge : -474.2569 centred at (gu) : 91.63258 94.36192 95.34447 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26555 grid for indexing accessible points = 1.400000 m= 26633 mr = 54168 m= 3602 mr = 19296 m= 124 mr = 2104 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 0.6800000 number of dielectric boundary points 33275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 23257 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) : 0.5966847 object centre at (A) : 22.74600 106.8775 131.7015 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4797861E-03 1.6925832E-02 midg,1,midg; midg,igrid,midg 3.8485818E-02 -8.1772506E-03 1,midg,midg; igrid,midg,midg -2.1807019E-02 -5.2416129E-03 gauss-seidel spectral radius is 0.9985037 estimated iterations to convergence 205 setup time was (sec) 0.9600000 now iterating at: 03:15:30 rms-change max change #iterations 4.159795 184.0553 at 10iterations 1.873133 68.70784 at 20iterations 0.8476822 32.06817 at 30iterations 0.3821626 13.98117 at 40iterations 0.1725690 5.613278 at 50iterations 7.8071743E-02 2.517431 at 60iterations 3.5335049E-02 1.092854 at 70iterations 1.5975798E-02 0.4961624 at 80iterations 7.2622602E-03 0.2577386 at 90iterations 3.3030345E-03 0.1004281 at 100iterations 1.5080622E-03 4.6187401E-02 at 110iterations 6.9822231E-04 2.3285866E-02 at 120iterations finished qdiffx linear iterations at : 03:15:39 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 6.9822231E-04 2.3285866E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.240000 DelPhi exited at 03:15:39 9.241u 0.295s 0:10.09 94.4% 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 03:15:39 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 = 3130 !!! WARNING: GLM 12 has a net charge of -0.0940 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: 2.685081 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): -0.9230000 46.41500 ymin,ymax (A): 77.04600 136.7090 zmin,zma (A): 102.2550 161.1480 x,y,z range (A): 47.33800 59.66300 58.89300 scale (grids/A): 2.685081 object centre (A): 22.74600 106.8775 131.7015 number of atom coordinates read : 3130 total number of charged atoms : 2987 net assigned charge : -7.093976 assigned positive charge : 467.1620 centred at (gu) : 92.75550 96.59586 98.03152 assigned negative charge : -474.2569 centred at (gu) : 92.44863 96.54278 98.01659 start vw surface at 0.1800000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 182314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26555 grid for indexing accessible points = 1.400000 m= 88296 mr = 132138 m= 29186 mr = 71446 m= 6105 mr = 23084 m= 646 mr = 4456 m= 13 mr = 396 m= 0 mr = 2 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2087 time to turn everything in is 1.740000 number of dielectric boundary points 75038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 23885 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) : 1.790054 object centre at (A) : 22.74600 106.8775 131.7015 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5197310E-02 0.7786424 midg,1,midg; midg,igrid,midg 0.8292156 -0.2990471 1,midg,midg; igrid,midg,midg -0.2962333 -4.2987030E-02 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 2.060000 now iterating at: 03:15:42 rms-change max change #iterations 10.18621 290.6439 at 10iterations 5.932761 145.9349 at 20iterations 3.433268 77.97478 at 30iterations 1.973107 40.91386 at 40iterations 1.135280 20.78663 at 50iterations 0.6502956 12.70695 at 60iterations 0.3720441 8.815766 at 70iterations 0.2125768 4.125612 at 80iterations 0.1215976 2.451393 at 90iterations 6.9388621E-02 1.220508 at 100iterations 3.9618012E-02 0.7725496 at 110iterations 2.2609213E-02 0.4190073 at 120iterations 1.2917848E-02 0.2599204 at 130iterations 7.3773246E-03 0.1306524 at 140iterations 4.2203092E-03 7.7533722E-02 at 150iterations 2.4310271E-03 4.9705505E-02 at 160iterations 1.4041181E-03 2.6585579E-02 at 170iterations 8.2037621E-04 1.6151428E-02 at 180iterations finished qdiffx linear iterations at : 03:15:56 total time elapsed so far: 15.51000 # loops : 180 mean,max change (kT/e) : 8.2037621E-04 1.6151428E-02 energy calculations done at 15.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.68000 DelPhi exited at 03:15:56 15.677u 0.279s 0:16.83 94.7% 0+0k 0+0io 0pf+0w