Tue Oct 11 01:40:23 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 01:40:23 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5933532 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): 18.17200 78.17000 ymin,ymax (A): -11.75100 44.12800 zmin,zma (A): -7.823000 35.17200 x,y,z range (A): 59.99800 55.87900 42.99500 scale (grids/A): 0.5933532 object centre (A): 48.17100 16.18850 13.67450 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : 8.312024 assigned positive charge : 408.6857 centred at (gu) : 88.42458 89.85931 89.91360 assigned negative charge : -400.3745 centred at (gu) : 88.69038 90.02734 90.02857 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6187 nv = 96 ne = 84 npr = 54171 no. pairs analyzed = 54171 no. exposed pairs = 3243 no. arc points = 23008 no. surface atoms = 1093 nbur = 1596 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= 268 mr = 3383 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2000000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2270 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3039867E-09 -8.1970197E-10 midg,1,midg; midg,igrid,midg 8.0019502E-09 -2.4275209E-09 1,midg,midg; igrid,midg,midg 1.5266041E-08 -3.8861452E-09 gauss-seidel spectral radius is 0.9853072 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 01:40:23 rms-change max change #iterations 0.1053747 18.74524 at 10iterations 9.4796959E-03 1.313141 at 20iterations 1.1564691E-03 0.2598839 at 30iterations 2.5208533E-04 5.9764862E-02 at 40iterations 5.9870650E-05 1.4953613E-02 at 50iterations finished qdiffx linear iterations at : 01:40:26 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.9870650E-05 1.4953613E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 01:40:27 3.408u 0.172s 0:03.89 91.7% 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 Oct 11 2011 at 01:40:27 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.780059 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): 18.17200 78.17000 ymin,ymax (A): -11.75100 44.12800 zmin,zma (A): -7.823000 35.17200 x,y,z range (A): 59.99800 55.87900 42.99500 scale (grids/A): 1.780059 object centre (A): 48.17100 16.18850 13.67450 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : 8.312024 assigned positive charge : 408.6857 centred at (gu) : 85.27312 89.57767 89.74027 assigned negative charge : -400.3745 centred at (gu) : 86.07092 90.08183 90.08547 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23008 grid for indexing accessible points = 1.400000 m= 22257 mr = 46684 m= 2981 mr = 16169 m= 91 mr = 1822 m= 0 mr = 18 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2941 time to turn everything in is 0.3300000 number of dielectric boundary points 28221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19806 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) : 0.5933532 object centre at (A) : 48.17100 16.18850 13.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2771724E-02 5.1239473E-03 midg,1,midg; midg,igrid,midg 2.7403124E-02 -2.4123162E-02 1,midg,midg; igrid,midg,midg 1.7093992E-02 2.2841920E-03 gauss-seidel spectral radius is 0.9984460 estimated iterations to convergence 201 setup time was (sec) 0.5500000 now iterating at: 01:40:28 rms-change max change #iterations 3.808830 175.0438 at 10iterations 1.693211 68.21743 at 20iterations 0.7519626 27.80165 at 30iterations 0.3329483 11.22763 at 40iterations 0.1485726 4.891174 at 50iterations 6.6298753E-02 2.428932 at 60iterations 2.9649185E-02 0.9438744 at 70iterations 1.3353188E-02 0.4459281 at 80iterations 6.0727103E-03 0.2463760 at 90iterations 2.8106151E-03 0.1017189 at 100iterations 1.3669910E-03 6.0565948E-02 at 110iterations 6.9959665E-04 2.8210640E-02 at 120iterations finished qdiffx linear iterations at : 01:40:35 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 6.9959665E-04 2.8210640E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 01:40:35 7.713u 0.194s 0:08.47 93.2% 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 01:40:35 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.670089 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): 18.17200 78.17000 ymin,ymax (A): -11.75100 44.12800 zmin,zma (A): -7.823000 35.17200 x,y,z range (A): 59.99800 55.87900 42.99500 scale (grids/A): 2.670089 object centre (A): 48.17100 16.18850 13.67450 number of atom coordinates read : 2689 total number of charged atoms : 2540 net assigned charge : 8.312024 assigned positive charge : 408.6857 centred at (gu) : 82.90970 89.36619 89.61034 assigned negative charge : -400.3745 centred at (gu) : 84.10621 90.12266 90.12813 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156668 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23008 grid for indexing accessible points = 1.400000 m= 74879 mr = 113668 m= 24628 mr = 60765 m= 5204 mr = 19556 m= 505 mr = 3906 m= 15 mr = 331 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 10193 time to turn everything in is 0.8200000 number of dielectric boundary points 63673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20313 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) : 1.780059 object centre at (A) : 48.17100 16.18850 13.67450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2506209 5.2049778E-02 midg,1,midg; midg,igrid,midg 0.3150001 -0.4545634 1,midg,midg; igrid,midg,midg 0.1363670 0.2274772 gauss-seidel spectral radius is 0.9992042 estimated iterations to convergence 280 setup time was (sec) 1.040000 now iterating at: 01:40:37 rms-change max change #iterations 9.120543 270.4745 at 10iterations 5.185031 154.7302 at 20iterations 2.928040 60.61252 at 30iterations 1.650259 34.59504 at 40iterations 0.9300126 20.17021 at 50iterations 0.5234929 11.01576 at 60iterations 0.2946571 5.905281 at 70iterations 0.1654413 3.088282 at 80iterations 9.3316272E-02 1.867886 at 90iterations 5.2516256E-02 1.063074 at 100iterations 2.9662156E-02 0.6851196 at 110iterations 1.6714090E-02 0.3465271 at 120iterations 9.5215039E-03 0.1874275 at 130iterations 5.4288600E-03 0.1052847 at 140iterations 3.1481879E-03 6.4620972E-02 at 150iterations 1.8768648E-03 4.4555664E-02 at 160iterations 1.1642062E-03 2.9544830E-02 at 170iterations 7.5473863E-04 1.9962311E-02 at 180iterations finished qdiffx linear iterations at : 01:40:48 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 7.5473863E-04 1.9962311E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 01:40:48 12.274u 0.219s 0:12.83 97.2% 0+0k 0+0io 0pf+0w